RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043239
(286 letters)
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific
2-hydroxyacid-related dehydrogenase.
Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the
NADP-dependent reduction of hydroxyphenylpyruvates,
hydroxypyruvate, or pyruvate to its respective lactate.
HPPR acts as a dimer and is related to D-isomer-specific
2-hydroxyacid dehydrogenases, a superfamily that
includes groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 301
Score = 307 bits (788), Expect = e-105
Identities = 106/238 (44%), Positives = 148/238 (62%), Gaps = 3/238 (1%)
Query: 17 FNPPLSERFTLLDPLLHSADSTHSFLSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVG 76
L RFT+ L +AD + L+ H +RA++ G + L++ ++ LPALE++
Sbjct: 13 LLAELEARFTVH-RLWEAADPA-ALLAEHGGRIRAVVTNGETGLSAALIAALPALELIAS 70
Query: 77 STAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPD 136
G D +DL R RGI VTN ++D AD VGLL+ VLRR+ + DRFVR G WP
Sbjct: 71 FGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAADRFVRAGRWP- 129
Query: 137 HGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPFYANVSGL 196
GA+PL + GKRVGIVGLG IG +A+RL FG IAY R+ KP V Y +YA++ L
Sbjct: 130 KGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEIAYHGRRPKPDVPYRYYASLLEL 189
Query: 197 AADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
AA+SDVL+V C T H++N +V+ ALG +GV++NV RG+++DE L+ L G +
Sbjct: 190 AAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGSVVDEAALIAALQEGRI 247
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 215 bits (550), Expect = 1e-68
Identities = 78/246 (31%), Positives = 123/246 (50%), Gaps = 7/246 (2%)
Query: 14 PGCFNPPLSERFTLLDPLLHSADSTHSFLSRHASSVRAILCLGPSPLTSDTLSLLPALEI 73
P L E+F + + + L+ A++ + ++ L LP L++
Sbjct: 12 PPEVLERLKEKFEVE--RYEDDLTPDTELAERLKDADAVITFVNDRIDAEVLEKLPGLKL 69
Query: 74 VVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGL 133
+ +AG D+VDL+ + RGI VTN +E A++ V L++ + RR+ DR VR G
Sbjct: 70 IATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEGDRRVREGN 129
Query: 134 WPDHGAY--PLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPF-- 189
W G LG L GK +GI+GLG IG VA+RL FG + Y R P
Sbjct: 130 WSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNPEAEKELGA 189
Query: 190 -YANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHF 248
Y ++ L A+SD++ + C LT ET H+IN + + + +++N RG L+DE+ L+
Sbjct: 190 RYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQALIDA 249
Query: 249 LVRGSL 254
L G +
Sbjct: 250 LKSGKI 255
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 309
Score = 189 bits (483), Expect = 8e-59
Identities = 78/221 (35%), Positives = 112/221 (50%), Gaps = 8/221 (3%)
Query: 38 THSFLSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVT 97
L A +LC + ++ L P L+++ + G DH+D+ + RGI VT
Sbjct: 33 PREELLEAAKGADGLLCTLTDKIDAELLDAAPPLKVIANYSVGYDHIDVDAAKARGIPVT 92
Query: 98 NAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYP---LGSTLGGKRVGIV 154
N + ++ AD LL+ RRV DRFVR G W G P LG+ L GK +GIV
Sbjct: 93 NTPDVLTDATADLAFALLLAAARRVVEGDRFVRAGEWK--GWSPTLLLGTDLHGKTLGIV 150
Query: 155 GLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPF---YANVSGLAADSDVLIVCCALTE 211
G+G IG VA+R FG I Y +R +KP Y ++ L A+SD + + C LT
Sbjct: 151 GMGRIGQAVARRAKGFGMKILYHNRSRKPEAEEELGARYVSLDELLAESDFVSLHCPLTP 210
Query: 212 ETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVRG 252
ET H+IN + + + ++IN RG ++DE LV L G
Sbjct: 211 ETRHLINAERLALMKPTAILINTARGGVVDEDALVEALKSG 251
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 189 bits (482), Expect = 9e-59
Identities = 79/227 (34%), Positives = 122/227 (53%), Gaps = 4/227 (1%)
Query: 31 LLHSADSTHSFLSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECR 90
++ + D L + A++ +P+T++ L+ P L+ + + AG+D++DL +
Sbjct: 24 VIVADDLLADELEALLADADALIVSSTTPVTAEVLAKAPKLKFIQVAGAGVDNIDLDAAK 83
Query: 91 RRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKR 150
+RGI VTN A +E A++ +GLL+ +LRR+ D VR G A G L GK
Sbjct: 84 KRGITVTNVPGANAEAVAEHALGLLLALLRRLPRADAAVRRGWG-WLWAGFPGYELEGKT 142
Query: 151 VGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVS---YPFYANVSGLAADSDVLIVCC 207
VGIVGLG IG VAKRL FG + Y R +KP ++ L A SDV+++
Sbjct: 143 VGIVGLGRIGQRVAKRLQAFGMKVLYYDRTRKPEPEEDLGFRVVSLDELLAQSDVVVLHL 202
Query: 208 ALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
LT ET H+IN++ + + V++N RG L+DE L+ L G +
Sbjct: 203 PLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDALLRALKSGKI 249
>gnl|CDD|240645 cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-like
dehydrogenases. D-Mandelate dehydrogenase (D-ManDH),
identified as an enzyme that interconverts
benzoylformate and D-mandelate, is a D-2-hydroxyacid
dehydrogenase family member that catalyzes the
conversion of c3-branched 2-ketoacids. D-ManDH exhibits
broad substrate specificities for 2-ketoacids with large
hydrophobic side chains, particularly those with
C3-branched side chains. 2-hydroxyacid dehydrogenases
catalyze the conversion of a wide variety of D-2-hydroxy
acids to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Glycerate dehydrogenase catalyzes the
reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH
+ H+. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 321
Score = 169 bits (430), Expect = 9e-51
Identities = 82/244 (33%), Positives = 114/244 (46%), Gaps = 13/244 (5%)
Query: 21 LSERFTLLDPLLHSADSTHSFLSRHA-SSVRAILCLGPS-----PLTSDTLSLLPA-LEI 73
LS ++ P + + L AI S P + +S LP L+I
Sbjct: 20 LSSIAEVIYPTSGTREEFIEALKEGKYGDFVAIYRTFGSAGETGPFDEELISPLPPSLKI 79
Query: 74 VVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGL 133
+ + AG D +D+ +RGI V+N A E AD + L++ LR S +R R G
Sbjct: 80 IAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERSARAGK 139
Query: 134 WPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKP----GVSYPF 189
W L GK +GI+GLG IG +A++ FG I Y +R + P +
Sbjct: 140 WRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLPEELEKALATY 199
Query: 190 YANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVII-NVGRGALIDEKELVHF 248
Y ++ L A SDV+ + C LT T H+INK A K+GVII N RGA+IDE LV
Sbjct: 200 YVSLDELLAQSDVVSLNCPLTAATRHLINKK-EFAKMKDGVIIVNTARGAVIDEDALVDA 258
Query: 249 LVRG 252
L G
Sbjct: 259 LESG 262
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 168 bits (428), Expect = 1e-50
Identities = 68/207 (32%), Positives = 109/207 (52%), Gaps = 6/207 (2%)
Query: 52 ILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYV 111
L + +P+T + L+ P L+ + + AG+D++DL+ +RGILV NA + A+ V
Sbjct: 48 ALIVSVTPVTEEVLAAAPNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELV 107
Query: 112 VGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFG 171
+ LL+ + RR+ D R G W G+ L GK VGI+GLG IG VAKRL FG
Sbjct: 108 LALLLALARRIPDADASQRRGEWDRKAFR--GTELAGKTVGIIGLGRIGRAVAKRLKAFG 165
Query: 172 CSIA----YTSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGK 227
+ Y+ R++ ++ L A++D+L + LT ET +IN + + +
Sbjct: 166 MKVIGYDPYSPRERAGVDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKP 225
Query: 228 EGVIINVGRGALIDEKELVHFLVRGSL 254
++IN RG ++DE L+ L G +
Sbjct: 226 GAILINAARGGVVDEDALLAALDSGKI 252
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 167 bits (425), Expect = 4e-50
Identities = 72/219 (32%), Positives = 114/219 (52%), Gaps = 14/219 (6%)
Query: 42 LSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGN 101
L ++ G P+T + L+ P L+++ G D++DL+ ++RGI+VTN
Sbjct: 41 LIELLKDADGVIA-GLDPITEEVLAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPG 99
Query: 102 AFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGS 161
A S A+ +GL++ + R++ DR VR G W P+G+ L GK +GI+GLG IG
Sbjct: 100 ANSNSVAELTIGLMLALARQIPQADREVRAGGWD----RPVGTELYGKTLGIIGLGRIGK 155
Query: 162 EVAKRLVPFGCSI-AY-----TSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHH 215
VA+RL FG + AY K+ GV + ++ L +SD + + LT ET H
Sbjct: 156 AVARRLSGFGMKVLAYDPYPDEEFAKEHGVE---FVSLEELLKESDFISLHLPLTPETRH 212
Query: 216 MINKDVMTALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
+IN + + ++IN RG L+DE+ L L G +
Sbjct: 213 LINAAELALMKPGAILINTARGGLVDEEALYEALKSGRI 251
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 317
Score = 160 bits (407), Expect = 2e-47
Identities = 65/220 (29%), Positives = 107/220 (48%), Gaps = 11/220 (5%)
Query: 38 THSFLSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVT 97
+ L + A++ +P+ + + L+I+ AG D++D+ + +GI VT
Sbjct: 33 SKEELLERIADYDALITPLSTPVDKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVT 92
Query: 98 NAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHG-AYPLGSTLGGKRVGIVGL 156
N +E A+ GL++ + RR++ DR +R G + + LG L GK +GI+G+
Sbjct: 93 NTPAVSTEPTAELTFGLILALARRIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGM 152
Query: 157 GSIGSEVAKRLVPFGCSIAYTSRKKKP-------GVSYPFYANVSGLAADSDVLIVCCAL 209
G IG VA+R FG I Y +R + G + Y ++ L +SD + +
Sbjct: 153 GRIGQAVARRAKAFGMKILYYNRHRLSEETEKELGAT---YVDLDELLKESDFVSLHAPY 209
Query: 210 TEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFL 249
T ETHH+I+ + +IN RG L+DEK LV L
Sbjct: 210 TPETHHLIDAAAFKLMKPTAYLINAARGPLVDEKALVDAL 249
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 158 bits (402), Expect = 1e-46
Identities = 66/204 (32%), Positives = 104/204 (50%), Gaps = 4/204 (1%)
Query: 52 ILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYV 111
L + +P+T++ + LP L+++V G+D+VD+ RGI V N + +E+ AD+
Sbjct: 47 ALLVQYAPVTAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHA 106
Query: 112 VGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFG 171
+ L++ + R++ +DR VR G W P+ L G +G+VG G IG VAKR FG
Sbjct: 107 LALILALARKLPFLDRAVRAGGWDWTVGGPIRR-LRGLTLGLVGFGRIGRAVAKRAKAFG 165
Query: 172 CSIAYTSRKKKPGVSYPFYANVSG---LAADSDVLIVCCALTEETHHMINKDVMTALGKE 228
+ GV+ V L A SDV+ + C LT ET H+I+ + + +
Sbjct: 166 FRVIAYDPYVPDGVAALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPG 225
Query: 229 GVIINVGRGALIDEKELVHFLVRG 252
++N RG L+DE L L G
Sbjct: 226 AFLVNTARGGLVDEAALARALKSG 249
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 311
Score = 152 bits (386), Expect = 2e-44
Identities = 75/205 (36%), Positives = 106/205 (51%), Gaps = 17/205 (8%)
Query: 60 LTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNA--GNAFSEDGADYVVGLLVD 117
+ ++ L+ P L ++ G+D VDL+ RGI V N GNA S A++ V L++
Sbjct: 55 IDAELLAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESV--AEHAVMLMLA 112
Query: 118 VLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYT 177
+LRR+ DR +R G W L GK VGIVGLG+IG VA+RL FG + Y
Sbjct: 113 LLRRLPEADRELRAGRWGR-PEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYY 171
Query: 178 SRKKKP-------GVSY-PFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEG 229
R + P GV Y L A+SDV+ + LT ET H+I + + A+
Sbjct: 172 DRFRDPEAEEKDLGVRYVELDE----LLAESDVVSLHVPLTPETRHLIGAEELAAMKPGA 227
Query: 230 VIINVGRGALIDEKELVHFLVRGSL 254
++IN RG L+DE+ L+ L G L
Sbjct: 228 ILINTARGGLVDEEALLAALRSGHL 252
>gnl|CDD|217244 pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydroxyacid
dehydrogenase, NAD binding domain. This domain is
inserted into the catalytic domain, the large
dehydrogenase and D-lactate dehydrogenase families in
SCOP. N-terminal portion of which is represented by
family pfam00389.
Length = 175
Score = 140 bits (356), Expect = 2e-41
Identities = 54/145 (37%), Positives = 75/145 (51%), Gaps = 4/145 (2%)
Query: 112 VGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFG 171
+ LL+ + RR+ DR VR G W LG L GK VGI+GLG IG VA+RL FG
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDA--LLGRELSGKTVGIIGLGRIGRAVARRLKAFG 58
Query: 172 CSIAYTSRKKKPGVS--YPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEG 229
+ R K Y ++ L A+SDV+ + LT ET H+IN + + +
Sbjct: 59 MKVIAYDRYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGA 118
Query: 230 VIINVGRGALIDEKELVHFLVRGSL 254
++IN RG L+DE L+ L G +
Sbjct: 119 ILINTARGGLVDEDALIAALKSGRI 143
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomains but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric. Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of plants.
Length = 313
Score = 142 bits (360), Expect = 2e-40
Identities = 66/245 (26%), Positives = 107/245 (43%), Gaps = 20/245 (8%)
Query: 17 FNPPLSERFTLLDPLLHSADSTHSFLSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVG 76
L + + +A+ L+ + +L P P + L P L +
Sbjct: 13 HLERLRAAAPGAELRVVTAEE----LTEELADADVLLGNPPLP---ELLPAAPRLRWIQS 65
Query: 77 STAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRN---GL 133
++AG+D + E R +++TNA F A+YV+G ++ R+ + R+ RN
Sbjct: 66 TSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARK---LPRYARNQAERR 122
Query: 134 WPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPFY--- 190
W G L GK V IVGLG IG E+A+R FG + R +P
Sbjct: 123 WQRRGPV---RELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVDEVYT 179
Query: 191 -ANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFL 249
+ L ++D ++ LT ET + N + A+ V+INVGRG+++DE L+ L
Sbjct: 180 PDELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDALIEAL 239
Query: 250 VRGSL 254
G +
Sbjct: 240 ESGRI 244
>gnl|CDD|240634 cd12157, PTDH, Thermostable Phosphite Dehydrogenase. Phosphite
dehydrogenase (PTDH), a member of the D-specific
2-hydroxyacid dehydrogenase family, catalyzes the
NAD-dependent formation of phosphate from phosphite
(hydrogen phosphonate). PTDH has been suggested as a
potential enzyme for cofactor regeneration systems. The
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD-binding
domain.
Length = 318
Score = 140 bits (355), Expect = 1e-39
Identities = 63/217 (29%), Positives = 107/217 (49%), Gaps = 4/217 (1%)
Query: 42 LSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGN 101
L R ++ P + +D L P L+I+ + G D+ D++ C RGI VT +
Sbjct: 38 LLRRCKDADGLMAFMPDRIDADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPD 97
Query: 102 AFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGS 161
+E A+ +GLL+ + R + + DRFVR+G + G+ L GK VGI+G+G++G
Sbjct: 98 LLTEPTAELTIGLLIGLGRHILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGR 157
Query: 162 EVAKRLVPFGCSIAYTSRKKKPGVSYPF----YANVSGLAADSDVLIVCCALTEETHHMI 217
+A+RL FG ++ Y + L SD L++ LT +T H+I
Sbjct: 158 AIARRLSGFGATLLYYDPHPLDQAEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLI 217
Query: 218 NKDVMTALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
N + + + +++N RG+++DE + L G L
Sbjct: 218 NAEALAKMKPGALLVNPCRGSVVDEAAVAEALKSGHL 254
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 140 bits (354), Expect = 2e-39
Identities = 74/212 (34%), Positives = 109/212 (51%), Gaps = 8/212 (3%)
Query: 49 VRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGA 108
V A++ + + + P L IV G D++D++E RRGI VTN +E A
Sbjct: 46 VDALVTMLSERIDCEVFEAAPRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATA 105
Query: 109 DYVVGLLVDVLRRVSSIDRFVRNGLWPDHGA--YP---LGSTLGGKRVGIVGLGSIGSEV 163
D+ LL+ RR+ D FVR+G W G +P LG + GK +GI+G G IG V
Sbjct: 106 DFAWALLLATARRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAV 165
Query: 164 AKRLVPFGCSIAYTSRKKKPGVSYPF---YANVSGLAADSDVLIVCCALTEETHHMINKD 220
A+R FG I Y SR +KP Y + L +SD + + LT+ET+HMIN++
Sbjct: 166 ARRAKGFGMRILYYSRTRKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEE 225
Query: 221 VMTALGKEGVIINVGRGALIDEKELVHFLVRG 252
+ + +++N RG ++D K LV L G
Sbjct: 226 RLKLMKPTAILVNTARGKVVDTKALVKALKEG 257
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 138 bits (350), Expect = 5e-39
Identities = 64/200 (32%), Positives = 102/200 (51%), Gaps = 15/200 (7%)
Query: 61 TSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNA--GNAFSEDGADYVVGLLVDV 118
T++ + P L+++ + G+D++D++ RGILV NA N S A++ + L++ +
Sbjct: 53 TAEVIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTIS--VAEHTIALMLAL 110
Query: 119 LRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCS-IAYT 177
R + D +R G W D + G L GK +GIVGLG IG EVA+R FG +AY
Sbjct: 111 ARNIPQADASLRAGKW-DRKKFM-GVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYD 168
Query: 178 -----SRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVII 232
R GV ++ L A++D + + LT ET +IN + + + ++I
Sbjct: 169 PYISAERAAAGGV---ELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILI 225
Query: 233 NVGRGALIDEKELVHFLVRG 252
N RG ++DE L L G
Sbjct: 226 NTARGGIVDEAALADALKSG 245
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 136 bits (346), Expect = 2e-38
Identities = 69/202 (34%), Positives = 107/202 (52%), Gaps = 9/202 (4%)
Query: 59 PLTSDTLSLLPALE-IVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVD 117
L ++ L+ LP L+ I V +T G ++VDL + RGI VTN ++ A + LL+
Sbjct: 54 VLDAEVLAQLPNLKLIGVLAT-GYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLA 112
Query: 118 VLRRVSSIDRFVRNGLW---PD--HGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGC 172
+ R V+ + V+ G W PD YP+ L GK +GI+G G+IG VA+ FG
Sbjct: 113 LARLVAYHNDVVKAGEWQKSPDFCFWDYPI-IELAGKTLGIIGYGNIGQAVARIARAFGM 171
Query: 173 SIAYTSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVII 232
+ + RK P + Y ++ L A SDV+ + C LT ET ++IN + + + ++I
Sbjct: 172 KVLFAERKGAPPLREG-YVSLDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILI 230
Query: 233 NVGRGALIDEKELVHFLVRGSL 254
N RG L+DE+ L L G +
Sbjct: 231 NTARGGLVDEQALADALNSGKI 252
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 134 bits (339), Expect = 2e-37
Identities = 60/224 (26%), Positives = 104/224 (46%), Gaps = 26/224 (11%)
Query: 44 RHASSVRAILCLGPSPLTSDTLSLLPALE-----IVVGSTAGIDHVDLQ---ECRRRGIL 95
++ LT + L AL+ V AG+DH+ L+ E G++
Sbjct: 36 EALEDADVLVG---GRLTKE--EALAALKRLKLIQVPS--AGVDHLPLERLPE----GVV 84
Query: 96 V-TNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWP-DHGAYPLGSTLGGKRVGI 153
V N GN S A++ + L++ + +R+ D +R G+W G P L GK VGI
Sbjct: 85 VANNHGN--SPAVAEHALALILALAKRIVEYDNDLRRGIWHGRAGEEPESKELRGKTVGI 142
Query: 154 VGLGSIGSEVAKRLVPFGCSI-AYTSRKKKPGVS--YPFYANVSGLAADSDVLIVCCALT 210
+G G IG E+A+ L FG + + K+ + +++ +DV++V LT
Sbjct: 143 LGYGHIGREIARLLKAFGMRVIGVSRSPKEDEGADFVGTLSDLDEALEQADVVVVALPLT 202
Query: 211 EETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
++T +I + A+ +++NVGRG ++DE+ L L +
Sbjct: 203 KQTRGLIGAAELAAMKPGAILVNVGRGPVVDEEALYEALKERPI 246
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 310
Score = 134 bits (339), Expect = 2e-37
Identities = 63/205 (30%), Positives = 93/205 (45%), Gaps = 11/205 (5%)
Query: 58 SPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAG--NAFSEDGADYVVGLL 115
+P+T + P L+++ G ++VD++ RGI V N NA + A++ VGL+
Sbjct: 55 APVTKKVIEAAPKLKLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAV--AEFTVGLM 112
Query: 116 VDVLRRVSSIDRFVRNGLWPDHGAYP---LGSTLGGKRVGIVGLGSIGSEVAKRLVPFGC 172
+ R ++ +++G W Y G L GK VGIVG G+IG VAKRL FG
Sbjct: 113 LAETRNIARAHAALKDGEW-RKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGA 171
Query: 173 SI-AYTSRKKKPGVSYPFYANVS--GLAADSDVLIVCCALTEETHHMINKDVMTALGKEG 229
+ Y + VS L SDV+ + LT ET MI + +
Sbjct: 172 EVLVYDPYVDPEKIEADGVKKVSLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTA 231
Query: 230 VIINVGRGALIDEKELVHFLVRGSL 254
IN R L+DE L+ L G +
Sbjct: 232 YFINTARAGLVDEDALIEALEEGKI 256
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family represents
the largest portion of the catalytic domain of
2-hydroxyacid dehydrogenases as the NAD binding domain
is inserted within the structural domain.
Length = 312
Score = 132 bits (335), Expect = 7e-37
Identities = 56/208 (26%), Positives = 89/208 (42%), Gaps = 9/208 (4%)
Query: 46 ASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSE 105
A A++ +P+T++ L P L+++ G+D++DL RGILVTN +E
Sbjct: 36 AKDADALIVRSTTPVTAEVLEAAPGLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTE 95
Query: 106 DGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAK 165
A+ VGL++ + RR+ D VR G W G P+G L GK +G++G G IG A
Sbjct: 96 SVAELTVGLILALARRIPEADASVRAGDWKKGG--PIGLELYGKTLGVIGGGGIGGIGAA 153
Query: 166 RLVPFGC-------SIAYTSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMIN 218
G ++ + L D++ + T +T H+I
Sbjct: 154 IAKALGMGVVAYDPYPNPERAEEGGVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIII 213
Query: 219 KDVMTALGKEGVIINVGRGALIDEKELV 246
+ L I N G +I+E L
Sbjct: 214 NEARGMLKDAVAINNARGGGVIEEAALD 241
>gnl|CDD|240620 cd01619, LDH_like, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-HicDH is a NAD-dependent member of the
hydroxycarboxylate dehydrogenase family, and shares the
Rossmann fold typical of many NAD binding proteins.
D-HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. Similar to the structurally
distinct L-HicDH, D-HicDH exhibits low side-chain R
specificity, accepting a wide range of 2-oxocarboxylic
acid side chains. (R)-2-hydroxyglutarate dehydrogenase
(HGDH) catalyzes the NAD-dependent reduction of
2-oxoglutarate to (R)-2-hydroxyglutarate.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 323
Score = 132 bits (334), Expect = 1e-36
Identities = 68/214 (31%), Positives = 102/214 (47%), Gaps = 6/214 (2%)
Query: 44 RHASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAF 103
A AIL + ++ L P L+ + G D++DL + GI VTN
Sbjct: 41 ELAKGADAILTAFTDKIDAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYS 100
Query: 104 SEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEV 163
A++ + L++ +LR ID +N D A +G L + VG+VG G IG V
Sbjct: 101 PNAVAEHTIALILALLRNRKYIDERDKNQDLQD--AGVIGRELEDQTVGVVGTGKIGRAV 158
Query: 164 AKRLVPFGCS-IAYTSRKKKPGVSYPF-YANVSGLAADSDVLIVCCALTEETHHMINKDV 221
A+R FG IAY + Y ++ L +SD++ + LT E HHMIN++
Sbjct: 159 AQRAKGFGMKVIAYDPFRNPELEDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEA 218
Query: 222 MTALGKEGVI-INVGRGALIDEKELVHFLVRGSL 254
L K+GVI IN RG+L+D + L+ L G +
Sbjct: 219 F-KLMKKGVIIINTARGSLVDTEALIEALDSGKI 251
>gnl|CDD|240644 cd12167, 2-Hacid_dh_8, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 330
Score = 130 bits (330), Expect = 6e-36
Identities = 72/243 (29%), Positives = 106/243 (43%), Gaps = 15/243 (6%)
Query: 21 LSERFTLLDPLLHSADSTHSFLSRHASSVRAIL-CLGPSPLTSDTLSLLPALEIVVGSTA 79
L+ +L P + + + + V ++ G PL ++ L+ P L VV A
Sbjct: 23 LAALAEVLPPTPDADFAAEELRAL-LAGVEVLVTGWGTPPLDAELLARAPRLRAVV-HAA 80
Query: 80 G--IDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDH 137
G V RGILVT+A +A +E A++ + ++ LRR+ R G
Sbjct: 81 GSVRGLVT-DAVWERGILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGW 139
Query: 138 GAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSI-AYT-----SRKKKPGVSYPFYA 191
G L G+ VGIVG G IG V + L PFG + Y + GV
Sbjct: 140 PTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDPYLPAAEAAALGVE---LV 196
Query: 192 NVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVR 251
++ L A SDV+ + LT ET MI+ ++ + IN RGAL+DE L+ L
Sbjct: 197 SLDELLARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEAALLAELRS 256
Query: 252 GSL 254
G L
Sbjct: 257 GRL 259
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 315
Score = 130 bits (328), Expect = 9e-36
Identities = 69/206 (33%), Positives = 107/206 (51%), Gaps = 7/206 (3%)
Query: 52 ILCLGPSPLTSDTLSLLPALE-IVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADY 110
I+ + PL + + L+ I V T G+DHVDL+ C+ RGI V+NA +E A+
Sbjct: 51 IVMIANMPLPGEVIEACKNLKMISVAFT-GVDHVDLEACKERGITVSNAAGYSTEAVAEL 109
Query: 111 VVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPF 170
+GL +D+LR + D VR G +G L GK VGIVG G+IG VA+ F
Sbjct: 110 TIGLAIDLLRNIVPCDAAVRAGGTKA---GLIGRELAGKTVGIVGTGAIGLRVARLFKAF 166
Query: 171 GCSIAYTSRKKKPGVSYPF--YANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKE 228
GC + SR +K Y ++ L A+SD++ + L +ET +I K+ + + +
Sbjct: 167 GCKVLAYSRSEKEEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKES 226
Query: 229 GVIINVGRGALIDEKELVHFLVRGSL 254
++IN RG ++D + L L G +
Sbjct: 227 AILINTARGPVVDNEALADALNEGKI 252
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 303
Score = 128 bits (325), Expect = 2e-35
Identities = 56/210 (26%), Positives = 91/210 (43%), Gaps = 10/210 (4%)
Query: 50 RAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDH-VDLQECRRRGILVTNAGNAFSEDGA 108
A++ G + + L P + V AG++ V+ G TNA A++E A
Sbjct: 30 DALVWTGSAREP-ERLPASPGVRWVQLPFAGVEAFVEAGVITDPGRRWTNAAGAYAETVA 88
Query: 109 DYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLV 168
++ + LL+ LR+ + R W L + L G V IVG G IG + L
Sbjct: 89 EHALALLLAGLRQ---LPARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPLLA 145
Query: 169 PFGCSIAYTSRKKKP----GVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTA 224
PFG + +R +P + P D+D +++ LT ET H+++ + A
Sbjct: 146 PFGAKVIAVNRSGRPVEGADETVPADRLDEVWP-DADHVVLAAPLTPETRHLVDAAALAA 204
Query: 225 LGKEGVIINVGRGALIDEKELVHFLVRGSL 254
+ ++NV RG L+D LV L G +
Sbjct: 205 MKPHAWLVNVARGPLVDTDALVDALRSGEI 234
>gnl|CDD|240632 cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2-hydroxyacid
dehydrogenase family. Phosphoglycerate Dehydrogenase
(PGDH) catalyzes the NAD-dependent conversion of
3-phosphoglycerate into 3-phosphohydroxypyruvate, which
is the first step in serine biosynthesis.
Over-expression of PGDH has been implicated as
supporting proliferation of certain breast cancers,
while PGDH deficiency is linked to defects in mammalian
central nervous system development. PGDH is a member of
the 2-hydroxyacid dehydrogenase family, enzymes that
catalyze the conversion of a wide variety of D-2-hydroxy
acids to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 314
Score = 128 bits (324), Expect = 3e-35
Identities = 52/182 (28%), Positives = 91/182 (50%), Gaps = 12/182 (6%)
Query: 79 AGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLW--PD 136
AG+D++ L+ +++GIL+TN S A+++VG ++++ + + + + W
Sbjct: 69 AGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLKKAYKNQKEKKWKMDS 128
Query: 137 HGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSI--AYTSRKKKPGVS--YPFYAN 192
L GK + +G GSIG E+AKRL FG + TS + YP
Sbjct: 129 SL-----LELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGRDVEYFDKCYPL-EE 182
Query: 193 VSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVRG 252
+ + ++D+++ LTEETHH+ ++ + K + INVGRG +DE L+ L
Sbjct: 183 LDEVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVGRGPSVDEDALIEALKNK 242
Query: 253 SL 254
+
Sbjct: 243 QI 244
>gnl|CDD|240663 cd12187, LDH_like_1, D-Lactate and related Dehydrogenase like
proteins, NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 125 bits (317), Expect = 5e-34
Identities = 66/209 (31%), Positives = 104/209 (49%), Gaps = 23/209 (11%)
Query: 58 SPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVD 117
S L ++ L LP L+++ + G DH+DL+ CR RGI V N + A++ LL+
Sbjct: 51 SRLDAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLA 110
Query: 118 VLRRV-SSIDR-----FVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFG 171
+ R++ +I+R F + GL G L GK +G+VG G IG VA+ FG
Sbjct: 111 LSRKLREAIERTRRGDFSQAGL--------RGFELAGKTLGVVGTGRIGRRVARIARGFG 162
Query: 172 CSI-AYTSRKKKP-----GVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTAL 225
+ AY + G Y ++ L +SD++ + T +THH+IN++ +
Sbjct: 163 MKVLAYDVVPDEELAERLGFRY---VSLEELLQESDIISLHVPYTPQTHHLINRENFALM 219
Query: 226 GKEGVIINVGRGALIDEKELVHFLVRGSL 254
V+IN RGA++D + LV L G L
Sbjct: 220 KPGAVLINTARGAVVDTEALVRALKEGKL 248
>gnl|CDD|240628 cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding
and catalytic domains. Phosphoglycerate dehydrogenase
(PGDH) catalyzes the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDH comes in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 301
Score = 122 bits (308), Expect = 6e-33
Identities = 63/190 (33%), Positives = 96/190 (50%), Gaps = 7/190 (3%)
Query: 69 PALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRF 128
L+I+ + G+D++D++ +++GI V N A S A+ V+GL++ + R + +R
Sbjct: 62 KNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANRE 121
Query: 129 VRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYP 188
++ G W Y G L GK +GI+G G IG EVAK G ++ K +
Sbjct: 122 MKLGKWN-KKKY-KGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPYPKDEQAVE 179
Query: 189 FYANVSGLA---ADSDVLIVCCALTEETHHMINKDVMTALGKEGV-IINVGRGALIDEKE 244
L +SD + + LT ET HMINK + L K+G IIN RG +IDE+
Sbjct: 180 LGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKEL-ELMKDGAIIINTSRGGVIDEEA 238
Query: 245 LVHFLVRGSL 254
L+ L G L
Sbjct: 239 LLEALKSGKL 248
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase. This model
represents a long form of D-3-phosphoglycerate
dehydrogenase, the serA gene of one pathway of serine
biosynthesis. Shorter forms, scoring between trusted and
noise cutoff, include SerA from E. coli [Amino acid
biosynthesis, Serine family].
Length = 525
Score = 123 bits (312), Expect = 3e-32
Identities = 68/209 (32%), Positives = 111/209 (53%), Gaps = 12/209 (5%)
Query: 51 AILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADY 110
A++ + +T + ++ P L+++ + G+D++D++ RGILV NA + A++
Sbjct: 43 ALIVRSATKVTEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEH 102
Query: 111 VVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPF 170
+ +L+ R + D ++ G W D A+ +G+ L GK +G++GLG IGS VAKR F
Sbjct: 103 ALAMLLAAARNIPQADASLKEGEW-DRKAF-MGTELYGKTLGVIGLGRIGSIVAKRAKAF 160
Query: 171 GCSI-AY-----TSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTA 224
G + AY R ++ GV ++ L A +D + V LT ET +I + + A
Sbjct: 161 GMKVLAYDPYISPERAEQLGVEL--VDDLDELLARADFITVHTPLTPETRGLIGAEEL-A 217
Query: 225 LGKEGVII-NVGRGALIDEKELVHFLVRG 252
K+GVII N RG +IDE L L G
Sbjct: 218 KMKKGVIIVNCARGGIIDEAALYEALEEG 246
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 122 bits (310), Expect = 7e-32
Identities = 67/182 (36%), Positives = 95/182 (52%), Gaps = 17/182 (9%)
Query: 80 GIDHVDLQECRRRGILVTNA--GNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDH 137
G+D+VD+ RRGI+V NA GN S A++ + L++ + R + ++ G W +
Sbjct: 74 GVDNVDVPAATRRGIIVVNAPTGNTIS--AAEHTIALMLALARNIPQAHASLKAGKW-ER 130
Query: 138 GAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCS-IAY-----TSRKKKPGVSYPFYA 191
+ +G L GK +GI+GLG IGSEVAKR FG IAY R + GV
Sbjct: 131 KKF-MGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDPYISPERAAQLGVE---LV 186
Query: 192 NVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGV-IINVGRGALIDEKELVHFLV 250
++ L A +D + + LT ET +I + + A K GV IIN RG +IDE L L
Sbjct: 187 SLDELLARADFITLHTPLTPETRGLIGAEEL-AKMKPGVRIINCARGGIIDEAALAEALK 245
Query: 251 RG 252
G
Sbjct: 246 SG 247
>gnl|CDD|240654 cd12177, 2-Hacid_dh_12, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 321
Score = 113 bits (286), Expect = 1e-29
Identities = 62/198 (31%), Positives = 102/198 (51%), Gaps = 6/198 (3%)
Query: 60 LTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDG-ADYVVGLLVDV 118
+ L+++ G D+VDL+ G++VT A D A++ V L++ V
Sbjct: 59 FDKEFFEYNDGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTV 118
Query: 119 LRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVP-FGCSI-AY 176
LR+++ V+ G W + + +G L GK VGI+G G+IGS VA+ L F + AY
Sbjct: 119 LRKINQASEAVKEGKWTERANF-VGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAY 177
Query: 177 --TSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINV 234
++ ++ L A+SD++ + LTEET+HMIN+ + + K +++N
Sbjct: 178 DPYVSEEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNT 237
Query: 235 GRGALIDEKELVHFLVRG 252
RG LIDE+ L+ L G
Sbjct: 238 ARGELIDEEALIEALKSG 255
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 112 bits (283), Expect = 5e-29
Identities = 58/217 (26%), Positives = 108/217 (49%), Gaps = 29/217 (13%)
Query: 60 LTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTN-----AGNAFSEDGADYVVGL 114
L +D ++ +++++ G++ VD+ + GI V GNA S A+ + L
Sbjct: 72 LDADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAAS--CAEMAIYL 129
Query: 115 LVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSI 174
++ +LR+ + + ++ G P+G TL GK V I+G G+IG E+AKRL PFG +
Sbjct: 130 MLGLLRKQNEMQISLKA---RRLGE-PIGDTLFGKTVFILGYGAIGIELAKRLRPFGVKL 185
Query: 175 AYTSRKKKPGVSYPFYANVSG-----------------LAADSDVLIVCCALTEETHHMI 217
T R+ +G A ++D++++CC LT+ET ++
Sbjct: 186 LAT-RRSWTSEPEDGLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETAGIV 244
Query: 218 NKDVMTALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
N + ++++ K +++N+ RG L+D ++ L G L
Sbjct: 245 NDEFLSSMKKGALLVNIARGGLLDYDAVLAALESGHL 281
>gnl|CDD|240661 cd12185, HGDH_LDH_like, Putative Lactate dehydrogenase and
(R)-2-Hydroxyglutarate Dehydrogenase-like proteins,
NAD-binding and catalytic domains. This group contains
various putative dehydrogenases related to D-lactate
dehydrogenase (LDH), (R)-2-hydroxyglutarate
dehydrogenase (HGDH), and related enzymes, members of
the 2-hydroxyacid dehydrogenases family. LDH catalyzes
the interconversion of pyruvate and lactate, and HGDH
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. Despite often low sequence
identity within this 2-hydroxyacid dehydrogenase family,
these proteins typically have a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD+ binding domain
is inserted within the linear sequence of the mostly
N-terminal catalytic domain, which has a similar domain
structure to the internal NAD binding domain.
Structurally, these domains are connected by extended
alpha helices and create a cleft in which NAD is bound,
primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 322
Score = 111 bits (280), Expect = 1e-28
Identities = 72/208 (34%), Positives = 103/208 (49%), Gaps = 22/208 (10%)
Query: 50 RAILCLGPSPLTSDTLSLLPALEIVVGST--AGIDHVDLQECRRRGILVTNAGNAFSEDG 107
I LG S ++++ L L + ST G DH+DL + GI V+N +S +
Sbjct: 46 DGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNV--TYSPNS 103
Query: 108 -ADYVVGLLVDVLRRVSSIDR------FVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIG 160
ADY V L++ LR+ I + + GL G L VG++G G IG
Sbjct: 104 VADYTVMLMLMALRKYKQIMKRAEVNDYSLGGL--------QGRELRNLTVGVIGTGRIG 155
Query: 161 SEVAKRLVPFGCSI-AYTSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINK 219
V K L FGC I AY + Y Y ++ L +SD++ + LTEET+H+INK
Sbjct: 156 QAVIKNLSGFGCKILAYDPYPNEEVKKYAEYVDLDTLYKESDIITLHTPLTEETYHLINK 215
Query: 220 DVMTALGKEGV-IINVGRGALIDEKELV 246
+ + A K+GV IIN RG LID + L+
Sbjct: 216 ESI-AKMKDGVIIINTARGELIDTEALI 242
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 110 bits (276), Expect = 2e-28
Identities = 65/199 (32%), Positives = 109/199 (54%), Gaps = 14/199 (7%)
Query: 60 LTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVL 119
+ + LS LP L+++ + G ++VD++ +++GI V N +E A + +L+ +L
Sbjct: 53 IDKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLL 112
Query: 120 RRVSSIDRFVRNGLWPD-----HGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSI 174
R++ DR+V++G + + H + PLG + GK+ GI+GLG+IG VAK FG +
Sbjct: 113 GRINYYDRYVKSGEYSESPIFTHISRPLG-EIKGKKWGIIGLGTIGKRVAKIAQAFGAKV 171
Query: 175 AY--TSRKKKPGVSYPFYANVS--GLAADSDVLIVCCALTEETHHMINKDVMTALGKEGV 230
Y TS K K Y VS L SD++ + L E+T ++I + L +
Sbjct: 172 VYYSTSGKNKN----EEYERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAI 227
Query: 231 IINVGRGALIDEKELVHFL 249
+INVGRG +++EK+L L
Sbjct: 228 LINVGRGGIVNEKDLAKAL 246
>gnl|CDD|240627 cd05302, FDH, NAD-dependent Formate Dehydrogenase (FDH).
NAD-dependent formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of a formate anion to carbon
dioxide coupled with the reduction of NAD+ to NADH.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxy acid dehydrogenase family have 2
highly similar subdomains of the alpha/beta form, with
NAD binding occurring in the cleft between subdomains.
NAD contacts are primarily to the Rossmann-fold
NAD-binding domain which is inserted within the linear
sequence of the more diverse flavodoxin-like catalytic
subdomain. Some related proteins have similar structural
subdomain but with a tandem arrangement of the catalytic
and NAD-binding subdomains in the linear sequence. FDHs
of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production from C1 compounds such as methanol,
and in the stress responses of plants. NAD-dependent FDH
is useful in cofactor regeneration in asymmetrical
biocatalytic reduction processes, where FDH irreversibly
oxidizes formate to carbon dioxide, while reducing the
oxidized form of the cofactor to the reduced form.
Length = 348
Score = 110 bits (276), Expect = 5e-28
Identities = 62/211 (29%), Positives = 102/211 (48%), Gaps = 21/211 (9%)
Query: 57 PSPLTSDTLSLLPALEIVVGSTAGI--DHVDLQECRRRGILVTNAGNAFSEDGADYVVGL 114
P+ +T++ ++ L++ + TAGI DHVDLQ RGI V + A++VV +
Sbjct: 71 PAYMTAERIAKAKNLKLAL--TAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMM 128
Query: 115 LVDVLRRVSSIDRFVRNGLW--PD--HGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPF 170
++ ++R G W D AY L GK VG VG G IG V +RL PF
Sbjct: 129 ILILVRNYVPGHEQAIEGGWNVADVVKRAY----DLEGKTVGTVGAGRIGLRVLRRLKPF 184
Query: 171 GCSIAYTSRKKKP-------GVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMT 223
+ Y R + P G++ +A++ + + DV+ + C L ET + NK++++
Sbjct: 185 DVHLLYYDRHRLPEEVEKELGLT--RHADLEDMVSKCDVVTINCPLHPETEGLFNKELLS 242
Query: 224 ALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
+ K ++N RG + D + + L G L
Sbjct: 243 KMKKGAYLVNTARGKICDREAVAEALESGHL 273
>gnl|CDD|240643 cd12166, 2-Hacid_dh_7, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 300
Score = 108 bits (273), Expect = 6e-28
Identities = 60/209 (28%), Positives = 96/209 (45%), Gaps = 16/209 (7%)
Query: 51 AILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVD--LQECRRRGILVTNAGNAFSEDGA 108
+ +P + L LP L +V +AG D V L E G+ + NA A
Sbjct: 41 VVPPYMAAPPVLEALRALPRLRVVQTLSAGYDGVLPLLPE----GVTLCNARGVHDASTA 96
Query: 109 DYVVGLLVDVLRRVSSIDRFVRN---GLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAK 165
+ V L++ LR + RFVR G W +L +RV IVG GSIG + +
Sbjct: 97 ELAVALILASLRG---LPRFVRAQARGRW----EPRRTPSLADRRVLIVGYGSIGRAIER 149
Query: 166 RLVPFGCSIAYTSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTAL 225
RL PF + +R +PG + L ++DV+++ LT+ET +++ + + +
Sbjct: 150 RLAPFEVRVTRVARTARPGEQVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARM 209
Query: 226 GKEGVIINVGRGALIDEKELVHFLVRGSL 254
+++NV RG ++D LV L G L
Sbjct: 210 PDGALLVNVARGPVVDTDALVAELASGRL 238
>gnl|CDD|240651 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 305
Score = 107 bits (270), Expect = 2e-27
Identities = 54/195 (27%), Positives = 98/195 (50%), Gaps = 15/195 (7%)
Query: 69 PALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRF 128
P+L+ + + AG++++D+ +RGI+V N A + A+ V+ +++ + R + ++
Sbjct: 49 PSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGANANAVAELVIAMMLALSRNIIQAIKW 108
Query: 129 VRNGLWPD-------HGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCS-IAY---- 176
V NG D +G+ L GK +G++GLG+IG VA + G I Y
Sbjct: 109 VTNGDGDDISKGVEKGKKQFVGTELRGKTLGVIGLGNIGRLVANAALALGMKVIGYDPYL 168
Query: 177 -TSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVI-INV 234
K V ++ L A +D + + LT+ET +IN +++ + K G I +N
Sbjct: 169 SVEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGLINAELLAKM-KPGAILLNF 227
Query: 235 GRGALIDEKELVHFL 249
RG ++DE+ L+ L
Sbjct: 228 ARGEIVDEEALLEAL 242
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 108 bits (271), Expect = 3e-27
Identities = 67/211 (31%), Positives = 105/211 (49%), Gaps = 21/211 (9%)
Query: 57 PSPLTSDTLSLLPALEIVVGSTAGI--DHVDLQECRRRGILVTNAGNAFSEDGADYVVGL 114
P+ LT++ ++ P L++ + TAGI DHVDLQ GI V + S A++VV +
Sbjct: 101 PAYLTAERIAKAPNLKLAI--TAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMM 158
Query: 115 LVDVLRRVSSIDRFVRNGLW--PDHG--AYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPF 170
++ ++R R G W D +Y L G VGIVG G IG V +RL PF
Sbjct: 159 ILALVRNYEPSHRQAVEGGWNIADCVSRSY----DLEGMTVGIVGAGRIGLAVLRRLKPF 214
Query: 171 GCSIAYTSRKKKP-------GVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMT 223
+ YT R + P G++Y + + L + DV+ + C L ET H+ + DV++
Sbjct: 215 DVKLHYTDRHRLPEEVEQELGLTY--HVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLS 272
Query: 224 ALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
+ + ++N RG ++D +V L G L
Sbjct: 273 RMKRGSYLVNTARGKIVDRDAVVRALESGHL 303
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 105 bits (264), Expect = 1e-26
Identities = 56/198 (28%), Positives = 93/198 (46%), Gaps = 5/198 (2%)
Query: 62 SDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRR 121
+ L +P L + G D+ D+ R IL+ + +E AD ++ L++ RR
Sbjct: 58 AALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARR 117
Query: 122 VSSIDRFVRNGLWPDH-GAYPLGSTLGGKRVGIVGLGSIGSEVAKRL-VPFGCSIAYTSR 179
V + V+ G W G G+ + K +GIVG+G IG +A+R F I Y +R
Sbjct: 118 VVEVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNAR 177
Query: 180 KKKPGVSYPF---YANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGR 236
+ F Y ++ L +SD + + LT+ETHH+ + + + IN GR
Sbjct: 178 RHHKEAEERFNARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAGR 237
Query: 237 GALIDEKELVHFLVRGSL 254
G ++DE L+ L +G +
Sbjct: 238 GPVVDENALIAALQKGEI 255
>gnl|CDD|240635 cd12158, ErythrP_dh, D-Erythronate-4-Phosphate Dehydrogenase
NAD-binding and catalytic domains.
D-Erythronate-4-phosphate Dehydrogenase (E. coli gene
PdxB), a D-specific 2-hydroxyacid dehydrogenase family
member, catalyzes the NAD-dependent oxidation of
erythronate-4-phosphate, which is followed by
transamination to form 4-hydroxy-L-threonine-4-phosphate
within the de novo biosynthesis pathway of vitamin B6.
D-Erythronate-4-phosphate dehydrogenase has the common
architecture shared with D-isomer specific 2-hydroxyacid
dehydrogenases but contains an additional C-terminal
dimerization domain in addition to an NAD-binding domain
and the "lid" domain. The lid domain corresponds to the
catalytic domain of phosphoglycerate dehydrogenase and
other proteins of the D-isomer specific 2-hydroxyacid
dehydrogenase family, which include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence.
Length = 343
Score = 104 bits (262), Expect = 4e-26
Identities = 60/193 (31%), Positives = 97/193 (50%), Gaps = 31/193 (16%)
Query: 75 VGS-TAGIDHVDLQECRRRGILVTNAG--NAFSEDGADYVVGLLVDVLRRVSSIDRFVRN 131
VG+ T G DH+D + RGI NA NA S A+YV+ L+
Sbjct: 61 VGTATIGTDHIDTDYLKERGIGFANAPGCNANSV--AEYVLSALL--------------- 103
Query: 132 GLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCS-IAYTSRKKKPGVSYPFY 190
A G +L GK VGIVG+G++GS +A+RL G + + + + F
Sbjct: 104 -----VLAQRQGFSLKGKTVGIVGVGNVGSRLARRLEALGMNVLLCDPPRAEAEGDPGF- 157
Query: 191 ANVSGLAADSDVLIVCCALTEE----THHMINKDVMTALGKEGVIINVGRGALIDEKELV 246
++ L A++D++ + LT + T+H++++D + AL ++IN RGA+ID + L+
Sbjct: 158 VSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGAVIDNQALL 217
Query: 247 HFLVRGSLVELVL 259
L RG + +VL
Sbjct: 218 ALLQRGKDLRVVL 230
>gnl|CDD|240659 cd12183, LDH_like_2, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2-domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 328
Score = 102 bits (258), Expect = 2e-25
Identities = 70/192 (36%), Positives = 101/192 (52%), Gaps = 32/192 (16%)
Query: 79 AGIDHVDLQECRRRGILVTNAGNAFSEDG-ADYVVGLLVDVLRRVS-SIDRFVR------ 130
AG ++VDL+ + GI V A+S A++ V LL+ + R++ + +R VR
Sbjct: 77 AGFNNVDLKAAKELGITVVRV-PAYSPYAVAEHAVALLLALNRKIHRAYNR-VREGNFSL 134
Query: 131 NGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSI----AYTSRK-KKPGV 185
+GL LG L GK VG++G G IG A+ L FGC + Y + + K GV
Sbjct: 135 DGL--------LGFDLHGKTVGVIGTGKIGQAFARILKGFGCRVLAYDPYPNPELAKLGV 186
Query: 186 SYPFYANVS--GLAADSDVLIVCCALTEETHHMINKDVMTALGKEGV-IINVGRGALIDE 242
Y V L A+SD++ + C LT ETHH+IN + + A K+GV +IN RG LID
Sbjct: 187 EY-----VDLDELLAESDIISLHCPLTPETHHLINAETI-AKMKDGVMLINTSRGGLIDT 240
Query: 243 KELVHFLVRGSL 254
K L+ L G +
Sbjct: 241 KALIEALKSGKI 252
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 306
Score = 99.3 bits (248), Expect = 3e-24
Identities = 57/174 (32%), Positives = 97/174 (55%), Gaps = 2/174 (1%)
Query: 79 AGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHG 138
AG++++DL+ + +GI + NA + ++ +G+L+ + +++ D+ VRNG+W G
Sbjct: 71 AGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRADQEVRNGIWDREG 130
Query: 139 AYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPFYANVSGLAA 198
G L GK VGI+G G++G AKRL FGC + + K G +Y ++ L
Sbjct: 131 NR--GVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGDAYAEQVSLETLFK 188
Query: 199 DSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVRG 252
++D+L + LT ET M+NK+ +++ K IN RG ++ K+LV L G
Sbjct: 189 EADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTKDLVKALKSG 242
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.
Phosphoglycerate dehydrogenases (PGDHs) catalyze the
initial step in the biosynthesis of L-serine from
D-3-phosphoglycerate. PGDHs come in 3 distinct
structural forms, with this first group being related to
2-hydroxy acid dehydrogenases, sharing structural
similarity to formate and glycerate dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily,
which also include groups such as L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Many, not all,
members of this family are dimeric.
Length = 308
Score = 98.7 bits (247), Expect = 3e-24
Identities = 59/198 (29%), Positives = 95/198 (47%), Gaps = 9/198 (4%)
Query: 59 PLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDV 118
P + L LP L+++V + +DL + RGI+V G A+ L++ +
Sbjct: 58 PFPAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGG-PTATAELTWALILAL 116
Query: 119 LRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCS-IAYT 177
R + D +R G W LG+ L GK +GIVGLG IG+ VA+ FG IA++
Sbjct: 117 ARNLPEEDAALRAGGWQTT----LGTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWS 172
Query: 178 SR-KKKPGVSYPFYANVS--GLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINV 234
S + + A VS L A SDV+ + L++ T ++ + + + +++N
Sbjct: 173 SNLTAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNT 232
Query: 235 GRGALIDEKELVHFLVRG 252
RG L+DE L+ L G
Sbjct: 233 SRGPLVDEGALLAALRAG 250
>gnl|CDD|240641 cd12164, GDH_like_2, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
also known as hydroxypyruvate reductase) and other
enzymes of the 2-hydroxyacid dehydrogenase family. GDH
catalyzes the reversible reaction of (R)-glycerate +
NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 306
Score = 96.4 bits (241), Expect = 3e-23
Identities = 61/216 (28%), Positives = 101/216 (46%), Gaps = 34/216 (15%)
Query: 46 ASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQE-------CRRRGILVTN 98
+ V L P P L+ LP L+ + AG+DH+ R + +
Sbjct: 37 PADVDYALVWKPPP---GLLARLPNLKAIFSLGAGVDHLLADPDLPDVPIVR-----LVD 88
Query: 99 AGNAFSEDGADYVVGLLVDVLRRVSSIDRFV---RNGLWPDHGAYPLGSTLGGKRVGIVG 155
G ++ A+YV+ ++ + R +DR+ R G+W P RVG++G
Sbjct: 89 PG--LAQGMAEYVLAAVLRLHRD---MDRYAAQQRRGVWKPLPQRPAAER----RVGVLG 139
Query: 156 LGSIGSEVAKRLVPFGCSIAYTSRKKK--PGVSYPFYANVSGLA---ADSDVLIVCCALT 210
LG +G+ VA+RL G ++ SR K GV+ F+ GL A +D+L+ LT
Sbjct: 140 LGELGAAVARRLAALGFPVSGWSRSPKDIEGVT-CFHGE-EGLDAFLAQTDILVCLLPLT 197
Query: 211 EETHHMINKDVMTALGKEGVIINVGRGALIDEKELV 246
ET ++N +++ L + +INVGRG + E +L+
Sbjct: 198 PETRGILNAELLARLPRGAALINVGRGPHLVEADLL 233
>gnl|CDD|240662 cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydroxyisocaproic
acid dehydrogenase (D-HicDH), NAD-binding and catalytic
domains. D-Lactate dehydrogenase (LDH) catalyzes the
interconversion of pyruvate and lactate, and is a member
of the 2-hydroxyacid dehydrogenases family. LDH is
homologous to D-2-hydroxyisocaproic acid
dehydrogenase(D-HicDH) and shares the 2 domain structure
of formate dehydrogenase. D-HicDH is a NAD-dependent
member of the hydroxycarboxylate dehydrogenase family,
and shares the Rossmann fold typical of many NAD binding
proteins. HicDH from Lactobacillus casei forms a monomer
and catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 95.3 bits (238), Expect = 9e-23
Identities = 62/185 (33%), Positives = 92/185 (49%), Gaps = 15/185 (8%)
Query: 78 TAGIDHVDLQECRRRGILVTNAGNAFSEDG-ADYVVGLLVDVLRRVSSIDRFVRNG--LW 134
+AG+D +DL + G+ +TN A+S A++ V +++LR IDR V G W
Sbjct: 76 SAGVDMIDLDLAKENGLKITNVP-AYSPRAIAEFAVTQALNLLRNTPEIDRRVAKGDFRW 134
Query: 135 PDHGAYPL-GSTLGGKRVGIVGLGSIGSEVAKRLVPFGCS-IAYTSRKKKPGV-SYPFYA 191
A L G + VGI+G G IGS AK FG IAY P + + Y
Sbjct: 135 ----APGLIGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKVIAY-DPYPNPELEKFLLYY 189
Query: 192 -NVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVI-INVGRGALIDEKELVHFL 249
++ L +D++ + LT+E HH+IN + A K+G I +N RG L+D K L+ L
Sbjct: 190 DSLEDLLKQADIISLHVPLTKENHHLINAEAF-AKMKDGAILVNAARGGLVDTKALIDAL 248
Query: 250 VRGSL 254
G +
Sbjct: 249 DSGKI 253
>gnl|CDD|240657 cd12180, 2-Hacid_dh_15, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 308
Score = 93.2 bits (232), Expect = 4e-22
Identities = 57/167 (34%), Positives = 88/167 (52%), Gaps = 13/167 (7%)
Query: 93 GILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVG 152
G +VT A +E A++V+ ++ +R+ I W PLGS L G +G
Sbjct: 85 GPVVTCARGVAAEAIAEFVLAAILAAAKRLPEI-WVKGAEQWRRE---PLGS-LAGSTLG 139
Query: 153 IVGLGSIGSEVAKRLVPFGCSIAYTSRKKKP----GVSYPFYANVSGLAADSDVLIVCCA 208
IVG G+IG +A+R + G + R +P GV A+++ L A SD L++
Sbjct: 140 IVGFGAIGQALARRALALGMRVLALRRSGRPSDVPGVEA--AADLAELFARSDHLVLAAP 197
Query: 209 LTEETHHMINKDVMTALGKEGV-IINVGRGALIDEKELVHFLVRGSL 254
LT ET H+IN DV+ A K G+ +IN+ RG L+D++ L+ L G +
Sbjct: 198 LTPETRHLINADVL-AQAKPGLHLINIARGGLVDQEALLEALDSGRI 243
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 91.8 bits (228), Expect = 1e-21
Identities = 60/217 (27%), Positives = 97/217 (44%), Gaps = 25/217 (11%)
Query: 60 LTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVL 119
T +TL+ LP L+++ + G ++VDL + GI V N S ++V+G++ +
Sbjct: 55 FTRETLAQLPKLKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALK 114
Query: 120 RRVSSIDRFVRNGLWPDHGA-----YPL----GSTLGGKRVGIVGLGSIGSEVAKRLVPF 170
+ R + W YP+ GSTLG + G G +G+EV +
Sbjct: 115 HSLMGWYRDQLSDRWATCKQFCYFDYPITDVRGSTLG-----VFGKGCLGTEVGRLAQAL 169
Query: 171 GCSIAYTSRKKKPGVS-----YPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTAL 225
G + Y K G S Y + V A D++ + C LTE T ++IN + + +
Sbjct: 170 GMKVLYAEHK---GASVCREGYTPFEEVLKQA---DIVTLHCPLTETTQNLINAETLALM 223
Query: 226 GKEGVIINVGRGALIDEKELVHFLVRGSLVELVLMCL 262
+IN GRG L+DE+ L+ L G + L L
Sbjct: 224 KPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVL 260
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 90.9 bits (226), Expect = 3e-21
Identities = 68/247 (27%), Positives = 102/247 (41%), Gaps = 26/247 (10%)
Query: 20 PLSERFTLLDPL-LHSADSTHSFLSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVGST 78
PL + F D L LH A + R + AI L + L+ P L++++ +
Sbjct: 20 PLEQAF---DELQLHDATTPEQVAERLRGAQVAIS--NKVALDAAALAAAPQLKLILVAA 74
Query: 79 AGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLW---- 134
G ++VDL R RGI V N + A + + LL+ + R+ + V G W
Sbjct: 75 TGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVAAGRWQQSS 134
Query: 135 ----PDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSI---AYTSRKKKPGVSY 187
D L GK +G++G G +G VA+ FG + R +P
Sbjct: 135 QFCLLDFPI----VELEGKTLGLLGHGELGGAVARLAEAFGMRVLIGQLPGRPARPD-RL 189
Query: 188 PFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVH 247
P L D L + C LTE T H+I + + ++IN RG L+DE+ L
Sbjct: 190 PLDE----LLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLVDEQALAD 245
Query: 248 FLVRGSL 254
L G L
Sbjct: 246 ALRSGHL 252
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 86.5 bits (214), Expect = 1e-19
Identities = 54/173 (31%), Positives = 89/173 (51%), Gaps = 7/173 (4%)
Query: 78 TAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDH 137
+AG+DH+D+ +L +NAG A+S A++ LL+ + + + ++NG +
Sbjct: 57 SAGVDHIDVSGIPENVVLCSNAG-AYSISVAEHAFALLLAWAKNICENNYNMKNGNF-KQ 114
Query: 138 GAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSI-AYTSRKKKPGVSYPFYANVSGL 196
L L K +GI+G G IG VA FG +I AYT G+S Y +
Sbjct: 115 SPTKL---LYNKSLGILGYGGIGRRVALLAKAFGMNIYAYTRSYVNDGISS-IYMEPEDI 170
Query: 197 AADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFL 249
SD +++ LT+ET MIN +++ K IINV R ++D+ ++++FL
Sbjct: 171 MKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLNFL 223
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 85.3 bits (211), Expect = 6e-19
Identities = 56/193 (29%), Positives = 98/193 (50%), Gaps = 25/193 (12%)
Query: 80 GIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGA 139
G ++VD++ + GI V N +E A+ L + RR+ D F+R GL+ G
Sbjct: 96 GYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY--EGW 153
Query: 140 YP---LGSTLGGKRVGIVGLGSIGSEVAKRLVP-FGCSIAY-----TSRKKK-------- 182
P +G+ L G+ VG++G G IGS A+ +V F ++ Y ++R +K
Sbjct: 154 LPHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFVTAYGQF 213
Query: 183 ------PGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGR 236
V++ +++ + ++DV+ + L + T+H+INK+ + + KE V++N R
Sbjct: 214 LKANGEQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNASR 273
Query: 237 GALIDEKELVHFL 249
G +IDE LV L
Sbjct: 274 GPVIDEVALVEHL 286
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 334
Score = 80.4 bits (199), Expect = 2e-17
Identities = 52/228 (22%), Positives = 83/228 (36%), Gaps = 28/228 (12%)
Query: 55 LGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQEC-RRRGILVTNAGNAFSEDGADYVVG 113
+ + +P L +V +AG DH + + + A A++V+G
Sbjct: 39 ILCTFHPHPDAEDVPNLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIG 98
Query: 114 LLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCS 173
+ + + W GKRVGI+G GSIG + A+ G
Sbjct: 99 TWLVLSHHFLQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGME 158
Query: 174 -IAYTSRKKK------------PGV-----SYP--FYANVSG------LAADSDVLIVCC 207
AYT + PG S P +++ L D D+L+V
Sbjct: 159 VYAYTRSPRPTPESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDLDLLVVSL 218
Query: 208 ALTEETHHMINKDVMTALGKEG-VIINVGRGALIDEKELVHFLVRGSL 254
LT T H++ + L K + N+ RG+L+D LV L G +
Sbjct: 219 PLTPATKHLLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQI 266
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 80.3 bits (198), Expect = 3e-17
Identities = 58/197 (29%), Positives = 92/197 (46%), Gaps = 19/197 (9%)
Query: 57 PSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLV 116
P+ +T++ + LE+++ + G DH+DL G+ V +E VV +
Sbjct: 108 PAYVTAERIKKAKNLELLLTAGIGSDHIDLPAAAAAGLTV-------AEVTGSNVVSVAE 160
Query: 117 DVLRRVSSIDR-F------VRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVP 169
D L R+ + R F V +G W G L GK VG VG G IG + +RL P
Sbjct: 161 DELMRILILLRNFLPGYHQVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKP 220
Query: 170 FGCSIAYTSRKKKPG-----VSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTA 224
F C++ Y R K F ++ + DV+++ LTE+T M NK+ +
Sbjct: 221 FNCNLLYHDRLKMDPELEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAK 280
Query: 225 LGKEGVIINVGRGALID 241
+ K +I+N RGA++D
Sbjct: 281 MKKGVLIVNNARGAIMD 297
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 78.4 bits (193), Expect = 1e-16
Identities = 48/191 (25%), Positives = 88/191 (46%), Gaps = 28/191 (14%)
Query: 78 TAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVR--NGLWP 135
TAG D DL ++ I+++N + E A+Y V + + ++RR I+R V+ + W
Sbjct: 77 TAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQAHDFTW- 135
Query: 136 DHGAYPLGST-LGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPFYAN-- 192
+ S + V I+G G IG+ AK FG +I +Y Y N
Sbjct: 136 ---QAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATI----------TAYDAYPNKD 182
Query: 193 ---------VSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEK 243
V D+D++ + +E++H+ +K + + K +++N RGA+I+
Sbjct: 183 LDFLTYKDSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTP 242
Query: 244 ELVHFLVRGSL 254
+L+ + G+L
Sbjct: 243 DLIAAVNDGTL 253
>gnl|CDD|240637 cd12160, 2-Hacid_dh_3, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 310
Score = 75.5 bits (186), Expect = 1e-15
Identities = 50/156 (32%), Positives = 75/156 (48%), Gaps = 9/156 (5%)
Query: 108 ADYVVGLLVDVLRRVSSIDRFVRNGLWPDH--GAYPLG-----STLGGKRVGIVGLGSIG 160
A++ + L++ +RR+ + R W G PL +TL G RV I G GSIG
Sbjct: 96 AEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIG 155
Query: 161 SEVAKRLVPFGCSIAYTSRKKKPGVSYPFYA--NVSGLAADSDVLIVCCALTEETHHMIN 218
+A L G + +R +P A + L ++DVL++ T T H ++
Sbjct: 156 QRLAPLLTALGARVTGVARSAGERAGFPVVAEDELPELLPETDVLVMILPATPSTAHALD 215
Query: 219 KDVMTALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
+V+ AL K ++NVGRGA +DE LV L G L
Sbjct: 216 AEVLAALPKHAWVVNVGRGATVDEDALVAALESGRL 251
>gnl|CDD|240653 cd12176, PGDH_3, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 73.4 bits (181), Expect = 5e-15
Identities = 49/179 (27%), Positives = 87/179 (48%), Gaps = 9/179 (5%)
Query: 80 GIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPD--H 137
G + VDL +RGI V NA + + A+ V+G ++ + RR+ + G+W
Sbjct: 74 GTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLARRLPDRNAAAHRGIWNKSAT 133
Query: 138 GAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIA-YTSRKKKP-GVSYPFYANVSG 195
G++ + GK +GI+G G IGS+++ G + Y +K P G + +++
Sbjct: 134 GSH----EVRGKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIAEKLPLGNARQ-VSSLEE 188
Query: 196 LAADSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
L A++D + + T T +MI + + + K ++IN RG ++D L L G L
Sbjct: 189 LLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRGTVVDIDALAEALRSGHL 247
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 72.1 bits (177), Expect = 1e-14
Identities = 49/205 (23%), Positives = 90/205 (43%), Gaps = 14/205 (6%)
Query: 59 PLTSDTLSLLPALEI--VVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLV 116
PL+ LL L I + +AG D DL+ + ++++N + E A++ V +
Sbjct: 56 PLSEAIYKLLNELGIKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAI 115
Query: 117 DVLRRVSSIDRFVR--NGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVP-FGCS 173
+++R + I VR + W L ++ +V ++G G IG VAK +G
Sbjct: 116 NLVRHFNQIQTKVREHDFRW---EPPILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSD 172
Query: 174 IA----YTSRKKKPGVSYPFYANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEG 229
+ + + K V Y + +D++ + T+ H++ N D+ K
Sbjct: 173 VVAYDPFPNAKAATYVDYK--DTIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGA 230
Query: 230 VIINVGRGALIDEKELVHFLVRGSL 254
V +N RG+L+D K L+ L G +
Sbjct: 231 VFVNCARGSLVDTKALLDALDNGLI 255
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 66.6 bits (163), Expect = 2e-12
Identities = 44/190 (23%), Positives = 82/190 (43%), Gaps = 28/190 (14%)
Query: 78 TAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDH 137
T G DH+DL GI ++A + DYV+G L+ ++ +
Sbjct: 66 TIGTDHLDLDYFAEAGITWSSAPGCNARGVVDYVLGSLL----TLAERE----------- 110
Query: 138 GAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFG--CSIAYTSRKKKPGVSYPFYANVSG 195
G L + G+VG G +G + + L G + R++ G + ++
Sbjct: 111 -----GVDLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCDPPRQEAEGDGD--FVSLER 163
Query: 196 LAADSDVLIVCCALTEE----THHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVR 251
+ + DV+ + LT+E T H++++ + +L +IN RGA++D + L L+
Sbjct: 164 ILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQALREALLS 223
Query: 252 GSLVELVLMC 261
G ++ VL
Sbjct: 224 GEDLDAVLDV 233
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 61.9 bits (150), Expect = 5e-11
Identities = 48/222 (21%), Positives = 86/222 (38%), Gaps = 20/222 (9%)
Query: 42 LSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGI--DHVDLQEC-RRRGILVTN 98
L++ S+ +L + PLT+ +L+ L + T I DH DL E R G+
Sbjct: 58 LAKALWSLDVVLKV-KEPLTNAEYALIQKLGDRLLFTYTIGADHRDLTEALARAGLTAIA 116
Query: 99 AGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGS 158
+G ++ I RF+ G P + GK V +VG G
Sbjct: 117 VEGVELPLLTSNSIGAGELSVQF---IARFLEVQQPGRLGGAP---DVAGKTVVVVGAGV 170
Query: 159 IGSEVAKRLVPFGCSIAYTSRK-------KKPGVSYPFYANVSGLAADSDVLIVCCALTE 211
+G E A+ L G + T ++ G + A++DV++ L
Sbjct: 171 VGKEAAQMLRGLGAQVLITDINVEALEQLEELGGK--NVEELEEALAEADVIVTTTLLPG 228
Query: 212 ETHHMIN-KDVMTALGKEGVIINVGRGALIDEKELVHFLVRG 252
+ ++ ++++ + VI+NV GA+ + L L+
Sbjct: 229 KRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEE 270
>gnl|CDD|240647 cd12170, 2-Hacid_dh_9, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 294
Score = 55.8 bits (135), Expect = 5e-09
Identities = 45/182 (24%), Positives = 70/182 (38%), Gaps = 37/182 (20%)
Query: 84 VDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLG 143
VD+ R GI VT + E +YV+ L+ +L +G
Sbjct: 86 VDIAAARENGITVTGIRDYGDEGVVEYVISELIRLL-----------HGFGG-KQWKEEP 133
Query: 144 STLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKP-----GVSYPFYANVSGLAA 198
L G +VGI+GLG+ G +A L FG + Y SR +KP G+ Y ++ L
Sbjct: 134 RELTGLKVGIIGLGTTGQMIADALSFFGADVYYYSRTRKPDAEAKGI---RYLPLNELLK 190
Query: 199 DSDVLIVCCALTEETHHMINKDVMT-------ALGKEGVIINVGRGALIDEKELVHFLVR 251
DV+ C + K+V+ LG ++ N G + + L +L
Sbjct: 191 TVDVICTC----------LPKNVILLGEEEFELLGDGKILFNTSLGPSFEVEALKKWLKA 240
Query: 252 GS 253
Sbjct: 241 SG 242
>gnl|CDD|240660 cd12184, HGDH_like, (R)-2-Hydroxyglutarate Dehydrogenase and
related dehydrogenases, NAD-binding and catalytic
domains. (R)-2-hydroxyglutarate dehydrogenase (HGDH)
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. HGDH is a member of the
D-2-hydroxyacid NAD(+)-dependent dehydrogenase family;
these proteins typically have a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD+ binding domain
is inserted within the linear sequence of the mostly
N-terminal catalytic domain, which has a similar domain
structure to the internal NAD binding domain.
Structurally, these domains are connected by extended
alpha helices and create a cleft in which NAD is bound,
primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 330
Score = 54.6 bits (132), Expect = 1e-08
Identities = 44/209 (21%), Positives = 80/209 (38%), Gaps = 7/209 (3%)
Query: 51 AILCLGPSPLTSDTLSLLPALEI--VVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGA 108
A++ G + L + I V T G +H+DL+ + G + + A
Sbjct: 47 AVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAIA 106
Query: 109 DYVVGLLVDVLRRVS-SIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRL 167
+ L + + R + + R D + + VGI+G G IG AK
Sbjct: 107 ELAFTLAMTLSRHTAYTASRTANKNFKVD--PFMFSKEIRNSTVGIIGTGRIGLTAAKLF 164
Query: 168 VPFGCS-IAYTSRKKKPGVSYPFYANVSGLAADSDVLIVCCA-LTEETHHMINKDVMTAL 225
G I Y + ++ L SD++ + + + +INK+ ++ +
Sbjct: 165 KGLGAKVIGYDIYPSDAAKDVVTFVSLDELLKKSDIISLHVPYIKGKNDKLINKEFISKM 224
Query: 226 GKEGVIINVGRGALIDEKELVHFLVRGSL 254
++IN RG L DE+ ++ L G L
Sbjct: 225 KDGAILINTARGELQDEEAILEALESGKL 253
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 52.5 bits (126), Expect = 6e-08
Identities = 34/107 (31%), Positives = 57/107 (53%), Gaps = 3/107 (2%)
Query: 151 VGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKK--PGV-SYPFYANVSGLAADSDVLIVCC 207
+GI+G G +GS+VA+ L +G + SR +K PGV S+ +S + + VLI
Sbjct: 139 IGILGAGVLGSKVAQSLQTWGFPLRCWSRSRKSWPGVQSFAGREELSAFLSQTRVLINLL 198
Query: 208 ALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELVHFLVRGSL 254
T ET +IN+ ++ L ++N+ RG + E +L+ L G +
Sbjct: 199 PNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKV 245
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 45.9 bits (110), Expect = 1e-05
Identities = 59/196 (30%), Positives = 85/196 (43%), Gaps = 43/196 (21%)
Query: 80 GIDHVDLQECRRRGILVTNA--GNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDH 137
G + VDL +RGI V NA N S A+ V+G ++ +LR + + G W +
Sbjct: 85 GTNQVDLDAAAKRGIPVFNAPFSNTRSV--AELVIGEIILLLRGIPEKNAKAHRGGW-NK 141
Query: 138 GAYPLGS-TLGGKRVGIVGLGSIGSEV---AKRLVPFGCSIAYTSRKKKPGVSYPFY--- 190
A GS + GK +GIVG G IG+++ A+ L G+ FY
Sbjct: 142 SA--AGSFEVRGKTLGIVGYGHIGTQLSVLAESL----------------GMRVYFYDIE 183
Query: 191 -----------ANVSGLAADSDVLIVCCALTEETHHMINKDVMTALGKEGVI-INVGRGA 238
++ L A SDV+ + T T +MI + + AL K G I IN RG
Sbjct: 184 DKLPLGNARQVGSLEELLAQSDVVSLHVPETPSTKNMIGAEEL-ALMKPGAILINASRGT 242
Query: 239 LIDEKELVHFLVRGSL 254
++D L L G L
Sbjct: 243 VVDIDALADALKSGHL 258
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 44.9 bits (106), Expect = 2e-05
Identities = 46/194 (23%), Positives = 84/194 (43%), Gaps = 24/194 (12%)
Query: 70 ALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSIDRFV 129
++ V +TAG DHVD ++ GI + A + +YV L+ + R D F
Sbjct: 58 PIKFVGTATAGTDHVDEAWLKQAGIGFSAAPGCNAIAVVEYVFSSLLMLAER----DGF- 112
Query: 130 RNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPF 189
+L + VGIVG+G++G + RL G +
Sbjct: 113 ---------------SLHDRTVGIVGVGNVGRRLQARLEALGIKTLLCDPPRADRGDEGD 157
Query: 190 YANVSGLAADSDVLIVCCALTEE----THHMINKDVMTALGKEGVIINVGRGALIDEKEL 245
+ ++ L ++D+L L ++ T H+ ++ ++ +L ++IN RGA++D L
Sbjct: 158 FRSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRGAVVDNTAL 217
Query: 246 VHFLVRGSLVELVL 259
+ L G + +VL
Sbjct: 218 LTCLNEGQKLSVVL 231
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 34.6 bits (80), Expect = 0.047
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 9/64 (14%)
Query: 150 RVGIVGLGSIGSEVAKRLVPFGCSIAYTSRK------KKPGVSYPFYANVSGLA-ADSDV 202
++GIVG G+ G +AK V G ++ TSR + GVS F+ + DV
Sbjct: 38 KIGIVGFGNFGQFLAKTFVKQGHTVLATSRSDYSDIAAELGVS--FFRDPDDFCEEHPDV 95
Query: 203 LIVC 206
+++C
Sbjct: 96 VLLC 99
>gnl|CDD|187627 cd05369, TER_DECR_SDR_a, Trans-2-enoyl-CoA reductase (TER) and
2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR.
TTER is a peroxisomal protein with a proposed role in
fatty acid elongation. Fatty acid synthesis is known to
occur in the both endoplasmic reticulum and
mitochondria; peroxisomal TER has been proposed as an
additional fatty acid elongation system, it reduces the
double bond at C-2 as the last step of elongation. This
system resembles the mitochondrial system in that
acetyl-CoA is used as a carbon donor. TER may also
function in phytol metabolism, reducting phytenoyl-CoA
to phytanoyl-CoA in peroxisomes. DECR processes double
bonds in fatty acids to increase their utility in fatty
acid metabolism; it reduces 2,4-dienoyl-CoA to an
enoyl-CoA. DECR is active in mitochondria and
peroxisomes. This subgroup has the Gly-rich NAD-binding
motif of the classical SDR family, but does not display
strong identity to the canonical active site tetrad, and
lacks the characteristic Tyr at the usual position. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 249
Score = 33.7 bits (78), Expect = 0.076
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 146 LGGKRVGIVGLGS-IGSEVAKRLVPFGCSIAYTSRKK 181
L GK I G G+ IG +AK G S+A RK
Sbjct: 1 LKGKVAFITGGGTGIGKAIAKAFAELGASVAIAGRKP 37
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 32.9 bits (76), Expect = 0.13
Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 17/100 (17%)
Query: 149 KRVGIVGLGSIGSEVAKRLVPFGCSI--------AYTSRKKKPGVSYPFYANVSGLAADS 200
++ +GLG +GS +A L+ G + G + A+ + AA++
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGAT--VAASPAEAAAEA 58
Query: 201 DVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALI 240
DV+I ++ G+ G++ + GA++
Sbjct: 59 DVVITMLPDDAAVRAVL-------FGENGLLEGLKPGAIV 91
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 33.0 bits (76), Expect = 0.16
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 12/92 (13%)
Query: 146 LGGKRVGIVGLGSIGSEVAKRLVPFGCS-IAYTSR--------KKKPGVSYPFYANVSGL 196
L K+V ++G G +G VAK L G I +R KK G +
Sbjct: 176 LKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAEELAKKLGAEAVALEELLEA 235
Query: 197 AADSDVLIVCCALTEETHHMINKDVMTALGKE 228
A++DV+I T H +I ++++ K
Sbjct: 236 LAEADVVISS---TSAPHPIITREMVERALKI 264
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 32.6 bits (75), Expect = 0.18
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 149 KRVGIVGLGSIGSEVAKRLVPFGCSIA 175
++ I+G G +G VA+ L G ++
Sbjct: 1 MKIIIIGAGRVGRSVARELSEEGHNVV 27
>gnl|CDD|216180 pfam00899, ThiF, ThiF family. This family contains a repeated
domain in ubiquitin activating enzyme E1 and members of
the bacterial ThiF/MoeB/HesA family.
Length = 134
Score = 31.4 bits (72), Expect = 0.24
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 149 KRVGIVGLGSIGSEVAKRLVPFGC 172
RV +VG G +GS A+ L G
Sbjct: 2 SRVLVVGAGGLGSPAAEYLARAGV 25
>gnl|CDD|238760 cd01483, E1_enzyme_family, Superfamily of activating enzymes (E1)
of the ubiquitin-like proteins. This family includes
classical ubiquitin-activating enzymes E1,
ubiquitin-like (ubl) activating enzymes and other
mechanistic homologes, like MoeB, Thif1 and others. The
common reaction mechanism catalyzed by MoeB, ThiF and
the E1 enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of MoaD, ThiS and ubiquitin,
respectively, on the alpha-phosphate of an ATP molecule
bound at the active site of the activating enzymes,
leading to the formation of a high-energy acyladenylate
intermediate and subsequently to the formation of a
thiocarboxylate at the C termini of MoaD and ThiS.
Length = 143
Score = 31.5 bits (72), Expect = 0.24
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 150 RVGIVGLGSIGSEVAKRLVPFGC 172
RV +VGLG +GSE+A L G
Sbjct: 1 RVLLVGLGGLGSEIALNLARSGV 23
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 31.1 bits (71), Expect = 0.25
Identities = 25/118 (21%), Positives = 47/118 (39%), Gaps = 16/118 (13%)
Query: 143 GSTLGGKRVGIVGLGSIGSEVAKRLVPFGCS---IAYTSRKK--------KPGVSYPFYA 191
L GK+V ++G G + AK L+ G IA + +K G
Sbjct: 7 FGDLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTLEKAKELAEEFPVGGEALPLD 66
Query: 192 NVSGLAADSDVLIVCCALTEETHHMINKDVMTALGK--EGVIINVGRGALIDEKELVH 247
+ L A++D++I T +I K+++ K + +++ I+ +EL
Sbjct: 67 ELEELLAEADIVISA---TSAPTPIITKEMVEEALKARPLLFVDIAVPRDIEPEELEG 121
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 32.3 bits (73), Expect = 0.29
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 150 RVGIVGLGSIGSEVAKRLVPFGCSIA------YTSRKKKPGVSYPFYANVSGLAADSDVL 203
++ IVG G+ G +AK +V G ++ Y+ +K GVSY +++ L + +
Sbjct: 371 KIAIVGFGNFGQFLAKTMVKQGHTVLAYSRSDYSDEAQKLGVSY--FSDADDLCEEHPEV 428
Query: 204 IVCC 207
I+ C
Sbjct: 429 ILLC 432
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 32.3 bits (74), Expect = 0.32
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 146 LGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKK 182
L GK+V +VG G G +AK L G + T K++
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILTDEKEE 39
>gnl|CDD|233182 TIGR00915, 2A0602, The (Largely Gram-negative Bacterial)
Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. Proteins
scoring above the trusted cutoff (1000) form a tight
clade within the RND (Resistance-Nodulation-Cell
Division) superfamily. Proteins scoring greater than the
noise cutoff (100) appear to form a larger clade,
cleanly separated from more distant homologs that
include cadmium/zinc/cobalt resistance transporters.
This family is one of several subfamilies within the
scope of Pfam model pfam00873 [Cellular processes, Toxin
production and resistance, Transport and binding
proteins, Unknown substrate].
Length = 1044
Score = 32.0 bits (73), Expect = 0.39
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 14/56 (25%)
Query: 87 QECRRRGILVTNAGNAF-------SEDG-------ADYVVGLLVDVLRRVSSIDRF 128
QE +R+G+ V A + F S DG +DY+ +VD + R+ +
Sbjct: 120 QEVQRQGVRVEKASSNFLMVIGLVSTDGSMTKEDLSDYIASNMVDPISRLEGVGDV 175
>gnl|CDD|238762 cd01485, E1-1_like, Ubiquitin activating enzyme (E1), repeat
1-like. E1, a highly conserved small protein present
universally in eukaryotic cells, is part of cascade to
attach ubiquitin (Ub) covalently to substrate proteins.
This cascade consists of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes and then targets them
for degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. The E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. A set of novel molecules
with a structural similarity to Ub, called Ub-like
proteins (Ubls), have similar conjugation cascades. In
contrast to ubiquitin-E1, which is a single-chain
protein with a weakly conserved two-fold repeat, many of
the Ubls-E1are a heterodimer where each subunit
corresponds to one half of a single-chain E1. This CD
represents the family homologous to the first repeat of
Ub-E1.
Length = 198
Score = 31.2 bits (71), Expect = 0.44
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 6/43 (13%)
Query: 126 DRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLV 168
DR +R LW D L S +V I+G G++G+E+AK LV
Sbjct: 3 DRQIR--LWGDEAQNKLRSA----KVLIIGAGALGAEIAKNLV 39
>gnl|CDD|237342 PRK13303, PRK13303, L-aspartate dehydrogenase; Provisional.
Length = 265
Score = 31.4 bits (72), Expect = 0.48
Identities = 24/105 (22%), Positives = 47/105 (44%), Gaps = 18/105 (17%)
Query: 149 KRVGIVGLGSIGSEVAKRL-----VPFGCSI----AYTSRKKKPGVSYPFYANVSGLAAD 199
+V ++G G+IG+ V + L + I + + ++ G + ++V L
Sbjct: 2 MKVAMIGFGAIGAAVLELLEHDPDLRVDWVIVPEHSIDAVRRALGEAVRVVSSVDALPQR 61
Query: 200 SDVLIVCCALTEETHHMINKDVMTAL--GKEGVIINVGRGALIDE 242
D+++ C H + + V+ L G + +I+V GAL DE
Sbjct: 62 PDLVVECAG-----HAALKEHVVPILKAGIDCAVISV--GALADE 99
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 31.0 bits (71), Expect = 0.52
Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 148 GKRVGIVG-LGSIGSEVAKRLVPFGC 172
GK + + G GSIGSE+ ++++ FG
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGP 27
>gnl|CDD|235783 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 31.2 bits (72), Expect = 0.64
Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 22/75 (29%)
Query: 150 RVGIVGLGSIGSEVAK-----------RLVPFGCSIAYT-----SRKKKPGV---SYPFY 190
+VG++GLG++GS V + R G I +K GV
Sbjct: 5 KVGLLGLGTVGSGVVRILEENAEEIAARA---GRPIEIKKVAVRDLEKDRGVDLPGILLT 61
Query: 191 ANVSGLAADSDVLIV 205
+ L D D+ IV
Sbjct: 62 TDPEELVNDPDIDIV 76
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 227
Score = 30.6 bits (70), Expect = 0.75
Identities = 25/87 (28%), Positives = 34/87 (39%), Gaps = 24/87 (27%)
Query: 142 LGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSI-------------------AYTSRKKK 182
LG L G RV I G G++GS A+ L G + A + KK+
Sbjct: 25 LGIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVAVSDSDGTIYNPDGLDVPALLAYKKE 84
Query: 183 PG--VSYP---FYANVSGLAADSDVLI 204
G + +P N L D D+LI
Sbjct: 85 HGSVLGFPGAERITNEELLELDCDILI 111
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 31.1 bits (71), Expect = 0.78
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 141 PLGSTLGGKRVGIVGL-GSIGSEVAKRLVPFGCS 173
+G+ L GK V + G GSIGSE+ ++++ F
Sbjct: 243 LIGAMLTGKTVLVTGGGGSIGSELCRQILKFNPK 276
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 29.5 bits (67), Expect = 0.88
Identities = 21/78 (26%), Positives = 28/78 (35%), Gaps = 13/78 (16%)
Query: 149 KRVGIVGLGSIGSEVAKRLV---PFGCSIAYTSR--------KKKPGVSYPFYANVSGLA 197
RVGIVG G IG + L + + GV P Y+++ L
Sbjct: 1 LRVGIVGAGKIGRRHLRALNESQDGAELVGILDPDPARAEAVAESFGV--PAYSDLEELL 58
Query: 198 ADSDVLIVCCALTEETHH 215
AD D+ V A H
Sbjct: 59 ADPDIDAVSVATPPGLHF 76
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 30.3 bits (69), Expect = 0.92
Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 11/97 (11%)
Query: 145 TLGGKRVGIVGLGSIGSEVAKRLVPFGCS-IAYTSRK--------KKPGVSYPFYANVSG 195
L GK+V ++G G +G AK L G + I +R K+ G + +
Sbjct: 175 NLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKELGGNAVPLDELLE 234
Query: 196 LAADSDVLIVCCALTEETHHMINKDVMTALGKEGVII 232
L ++DV+I A + I + M + +I
Sbjct: 235 LLNEADVVI--SATGAPHYAKIVERAMKKRSGKPRLI 269
>gnl|CDD|215463 PLN02858, PLN02858, fructose-bisphosphate aldolase.
Length = 1378
Score = 31.0 bits (70), Expect = 1.00
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 13/69 (18%)
Query: 149 KRVGIVGLGSIGSEVAKRLVPFG-CSIAYTSRKKKPGVSYPFYANVSGLAADS------- 200
KR+G +GLG++G +A L+ Y KP + + N GLA +S
Sbjct: 325 KRIGFIGLGAMGFGMASHLLKSNFSVCGYDV--YKPTLVR--FENAGGLAGNSPAEVAKD 380
Query: 201 -DVLIVCCA 208
DVL++ A
Sbjct: 381 VDVLVIMVA 389
>gnl|CDD|237341 PRK13302, PRK13302, putative L-aspartate dehydrogenase;
Provisional.
Length = 271
Score = 30.2 bits (68), Expect = 1.1
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 17/108 (15%)
Query: 150 RVGIVGLGSIGSEVAKRLV--PFGCSIAYTSRKKKPGVSYPFYAN---------VSGLAA 198
RV I GLG+IG +A+ L G +++ + + P F + LA
Sbjct: 8 RVAIAGLGAIGKAIAQALDRGLPGLTLSAVA-VRDPQRHADFIWGLRRPPPVVPLDQLAT 66
Query: 199 DSDVLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALIDEKELV 246
+D+++ I + V+ A GK+ ++++V GAL+ ++L+
Sbjct: 67 HADIVVEAAP--ASVLRAIVEPVLAA-GKKAIVLSV--GALLRNEDLI 109
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 28.7 bits (65), Expect = 1.1
Identities = 12/69 (17%), Positives = 26/69 (37%), Gaps = 14/69 (20%)
Query: 150 RVGIVGLGSIGSEVAKRL------VPFGCS-----IAYTSRKKKPGVSYPFYANVSGLAA 198
++GI+G G++G +A+ L V S A + + +
Sbjct: 1 KIGIIGAGNMGEALARGLAAAGHEVVIANSRNPEKAAALAEELGVKATAVSNEEA---VE 57
Query: 199 DSDVLIVCC 207
++DV+ +
Sbjct: 58 EADVVFLAV 66
>gnl|CDD|132290 TIGR03246, arg_catab_astC, succinylornithine transaminase family.
Members of the seed alignment for this protein family
are the enzyme succinylornithine transaminase (EC
2.6.1.81), which catalyzes the third of five steps in
arginine succinyltransferase (AST) pathway, an
ammonia-releasing pathway of arginine degradation. All
seed alignment sequences are found within arginine
succinyltransferase operons, and all proteins that score
above 820.0 bits should function as succinylornithine
transaminase. However, a number of sequences extremely
closely related in sequence, found in different genomic
contexts, are likely to act in different biological
processes and may act on different substrates. This
model is desigated subfamily rather than equivalog,
pending further consideration, for this reason [Energy
metabolism, Amino acids and amines].
Length = 397
Score = 30.1 bits (68), Expect = 1.2
Identities = 28/123 (22%), Positives = 48/123 (39%), Gaps = 20/123 (16%)
Query: 137 HGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPFYANVSGL 196
+G PL + GK + +V + + V +R + +K Y ++ + G
Sbjct: 278 YGGNPLACAVAGKVLDLVNTPELLAGVKQR------HDLFVDGLEKINARYNVFSEIRGK 331
Query: 197 AADSDVLIVCCALTEETHHMINKDVMTALGKEGVII-----NVGRGA---LIDEKELVHF 248
L++ LTE K + A +EGVI NV R A +I + ++
Sbjct: 332 G-----LLIGAVLTEAYQGK-AKQFVNAAAEEGVIALIAGPNVVRFAPSLVISDDDIDEG 385
Query: 249 LVR 251
L R
Sbjct: 386 LAR 388
>gnl|CDD|238770 cd01493, APPBP1_RUB, Ubiquitin activating enzyme (E1) subunit
APPBP1. APPBP1 is part of the heterodimeric activating
enzyme (E1), specific for the Rub family of
ubiquitin-like proteins (Ubls). E1 enzymes are part of a
conjugation cascade to attach Ub or Ubls, covalently to
substrate proteins consisting of activating (E1),
conjugating (E2), and/or ligating (E3) enzymes. E1
activates ubiquitin(-like) by C-terminal adenylation,
and subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis.
ABPP1 contains part of the adenylation domain.
Length = 425
Score = 30.4 bits (69), Expect = 1.2
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 126 DRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGSIGSEVAKRLV 168
DR +R LW +HG L S V ++ + G+E+ K LV
Sbjct: 4 DRQLR--LWGEHGQAALESA----HVCLLNATATGTEILKNLV 40
>gnl|CDD|180317 PRK05942, PRK05942, aspartate aminotransferase; Provisional.
Length = 394
Score = 30.1 bits (68), Expect = 1.3
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 93 GILVTNAGNAFSEDGADYV-VGLLVDVLRRVSSIDRFVRNGL 133
G++VT GNAF E G YV + L+ D R ++DR + G+
Sbjct: 351 GVVVT-PGNAFGEGGEGYVRISLIADCDRLGEALDRLKQAGI 391
>gnl|CDD|236190 PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase;
Validated.
Length = 252
Score = 29.9 bits (68), Expect = 1.3
Identities = 18/59 (30%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 148 GKRVGIVGLGS-IGSEVAKRLVPFGCSIAYTSRKKKPGVSYPF---YANVSGLAADSDV 202
GK V + G IG VA V G + + YPF +VS AA + V
Sbjct: 8 GKTVWVTGAAQGIGYAVALAFVEAGAKVIGFDQAFLTQEDYPFATFVLDVSDAAAVAQV 66
>gnl|CDD|183197 PRK11559, garR, tartronate semialdehyde reductase; Provisional.
Length = 296
Score = 30.0 bits (68), Expect = 1.4
Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 16/99 (16%)
Query: 149 KRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKP-------GVSYPFYANVSGLAADSD 201
+VG +GLG +G ++K L+ G S+ R + G + +A D
Sbjct: 3 MKVGFIGLGIMGKPMSKNLLKAGYSLVVYDRNPEAVAEVIAAGAETA--STAKAVAEQCD 60
Query: 202 VLIVCCALTEETHHMINKDVMTALGKEGVIINVGRGALI 240
V+I + + H+ K+V ALG+ G+I G ++
Sbjct: 61 VII---TMLPNSPHV--KEV--ALGENGIIEGAKPGTVV 92
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine
dehydrogenase, phenylalanine dehydrogenase, and valine
dehydrogenase. Amino acid dehydrogenase (DH) is a
widely distributed family of enzymes that catalyzes the
oxidative deamination of an amino acid to its keto acid
and ammonia with concomitant reduction of NADP+. For
example, leucine DH catalyzes the reversible oxidative
deamination of L-leucine and several other straight or
branched chain amino acids to the corresponding
2-oxoacid derivative. Amino acid DH -like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 200
Score = 29.5 bits (67), Expect = 1.6
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 145 TLGGKRVGIVGLGSIGSEVAKRL 167
+L GK V + GLG +G ++A+ L
Sbjct: 25 SLEGKTVAVQGLGKVGYKLAEHL 47
>gnl|CDD|237612 PRK14108, PRK14108, bifunctional glutamine-synthetase
adenylyltransferase/deadenyltransferase; Provisional.
Length = 986
Score = 30.0 bits (68), Expect = 1.9
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 17/63 (26%)
Query: 99 AGNAFSEDGADYVVGLLVDVLRRVSSIDRFVRNGLWPDHGAYPLGSTLGGKRVGIVGLGS 158
AG AF+ D A+ ++G L V + F R HG G RV I+ +G
Sbjct: 667 AGRAFA-DLAELIIG---AALDAVE--EEFARA-----HGRIK------GGRVAILAMGK 709
Query: 159 IGS 161
+GS
Sbjct: 710 LGS 712
>gnl|CDD|176186 cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 29.0 bits (66), Expect = 3.2
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 148 GKRVGIVGLGSIGSEVAKRLVPFGCS-IAYTSRKKK 182
GKRVG+VG+G +G K G A++ K
Sbjct: 170 GKRVGVVGIGGLGHLAVKFAKALGAEVTAFSRSPSK 205
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 27.9 bits (63), Expect = 3.3
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 9/38 (23%)
Query: 161 SEVAKRLV-----PFGCSIAYTSRKKKP----GVSYPF 189
S + KRL+ FG S+++T+RK +P GV Y F
Sbjct: 13 STLLKRLLEEFDPNFGFSVSHTTRKPRPGEVDGVDYHF 50
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 28.6 bits (65), Expect = 3.5
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 143 GSTLGGKRVGIVGLGSIGSEVAKRLVPFG 171
G +L GK V + G G++GS A++L+ G
Sbjct: 27 GDSLEGKTVAVQGFGNVGSYAAEKLLELG 55
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 28.5 bits (64), Expect = 3.6
Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 10/91 (10%)
Query: 149 KRVGIVGLGSIGSEVAKRLVPFGCSIAYTSR---KKKPGVSYPFYANVSGL-----AADS 200
+ I+G G+IGS +A RL G + S K + ++G AA +
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVIIGSSRGPKALAAAAAALGPLITGGSNEDAAALA 61
Query: 201 DVLIVCCALTEETHHMINKDVMTALGKEGVI 231
DV+++ A+ E + ++ ALG + VI
Sbjct: 62 DVVVL--AVPFEAIPDVLAELRDALGGKIVI 90
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 28.4 bits (64), Expect = 3.7
Identities = 18/69 (26%), Positives = 26/69 (37%), Gaps = 10/69 (14%)
Query: 149 KRVGIVGLGSIGSEVA---KRLVPFGCSIAYT------SRKKKPGVSYPFYANVS-GLAA 198
+VGIVGLG +G +A K I + GV AA
Sbjct: 4 MKVGIVGLGLMGGSLARALKEAGLVVRIIGRDRSAATLKAALELGVIDELTVAGLAEAAA 63
Query: 199 DSDVLIVCC 207
++D++IV
Sbjct: 64 EADLVIVAV 72
>gnl|CDD|237343 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 28.4 bits (64), Expect = 3.8
Identities = 29/107 (27%), Positives = 52/107 (48%), Gaps = 19/107 (17%)
Query: 150 RVGIVGLGSIGSEVAKRLVP--FGCSIAY---TSRKKKPGVSY----PFYANVSGLAADS 200
++GIVG G+I S + K ++ + + +K ++ ++ L D
Sbjct: 3 KIGIVGCGAIASLITKAILSGRINAELYAFYDRNLEKAENLASKTGAKACLSIDELVEDV 62
Query: 201 DVLIVCCALTEETHHMINKDVMTAL--GKEGVIINVGRGALIDEKEL 245
D L+V CA + + + + V +L GK+ +I++V GAL D KEL
Sbjct: 63 D-LVVECA----SVNAVEEVVPKSLENGKDVIIMSV--GALAD-KEL 101
>gnl|CDD|222002 pfam13241, NAD_binding_7, Putative NAD(P)-binding. This domain is
found in fungi, plants, archaea and bacteria.
Length = 104
Score = 27.0 bits (61), Expect = 4.0
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 146 LGGKRVGIVGLGSIGSEVAKRLVPFGCSI 174
L GKRV +VG G + + L+ G +
Sbjct: 5 LKGKRVLVVGGGEVALRKIRALLEAGAKV 33
>gnl|CDD|224805 COG1893, ApbA, Ketopantoate reductase [Coenzyme metabolism].
Length = 307
Score = 28.4 bits (64), Expect = 4.3
Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 16/74 (21%)
Query: 150 RVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKK----------------PGVSYPFYANV 193
++ I+G G+IGS + RL G + R ++ + A
Sbjct: 2 KILILGAGAIGSLLGARLAKAGHDVTLLVRSRRLEALKKKGLRIEDEGGNFTTPVVAATD 61
Query: 194 SGLAADSDVLIVCC 207
+ +D++IV
Sbjct: 62 AEALGPADLVIVTV 75
>gnl|CDD|180667 PRK06718, PRK06718, precorrin-2 dehydrogenase; Reviewed.
Length = 202
Score = 28.1 bits (63), Expect = 4.6
Identities = 19/89 (21%), Positives = 31/89 (34%), Gaps = 28/89 (31%)
Query: 140 YPLGSTLGGKRVGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPFYANVSGLAAD 199
PL L KRV IVG G +VA R+ + Y
Sbjct: 2 MPLMIDLSNKRVVIVG----GGKVA-------------GRRAITLLKY-----------G 33
Query: 200 SDVLIVCCALTEETHHMINKDVMTALGKE 228
+ ++++ LTE ++ + + KE
Sbjct: 34 AHIVVISPELTENLVKLVEEGKIRWKQKE 62
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP kinase.
This enzyme transfers a phosphate from ATP to GMP,
yielding ADP and GDP [Purines, pyrimidines, nucleosides,
and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 27.8 bits (63), Expect = 4.7
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 154 VGLGSIGSEVAKRLVPFGCSIAYTSRKKKP----GVSYPF 189
G ++ + + SI+ T+RK +P GV Y F
Sbjct: 11 AGKSTLVKALLEEDPNLKFSISATTRKPRPGEVDGVDYFF 50
>gnl|CDD|238769 cd01492, Aos1_SUMO, Ubiquitin activating enzyme (E1) subunit Aos1.
Aos1 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. Aos1
contains part of the adenylation domain.
Length = 197
Score = 28.0 bits (63), Expect = 4.9
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 150 RVGIVGLGSIGSEVAKRLV 168
R+ ++GL +G+E+AK LV
Sbjct: 23 RILLIGLKGLGAEIAKNLV 41
>gnl|CDD|136048 PRK06781, PRK06781, amidophosphoribosyltransferase; Provisional.
Length = 471
Score = 28.4 bits (63), Expect = 5.5
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 5/92 (5%)
Query: 148 GKRVGIVGLGSIGSEVAKRLVPFGCSIAYTS---RKKKPGVSYPFYANVSGLAADSDVLI 204
GKRV ++ + +KR+V T R P + YP + + LI
Sbjct: 348 GKRVVMIDDSIVRGTTSKRIVRMLREAGATEVHVRIASPPLKYPCFYGID--IQTRKELI 405
Query: 205 VCCALTEETHHMINKDVMTALGKEGVIINVGR 236
EE MI D +T L ++G++ +GR
Sbjct: 406 AANHTVEEIREMIGADSLTFLSEDGLVDAIGR 437
>gnl|CDD|187620 cd05362, THN_reductase-like_SDR_c,
tetrahydroxynaphthalene/trihydroxynaphthalene
reductase-like, classical (c) SDRs.
1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) of
Magnaporthe grisea and the related
1,3,8-trihydroxynaphthalene reductase (3HNR) are typical
members of the SDR family containing the canonical
glycine rich NAD(P)-binding site and active site tetrad,
and function in fungal melanin biosynthesis. This
subgroup also includes an SDR from Norway spruce that
may function to protect against both biotic and abitoic
stress. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 243
Score = 28.0 bits (63), Expect = 5.5
Identities = 17/41 (41%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 146 LGGKRVGIVGLGS--IGSEVAKRLVPFGCSIA--YTSRKKK 182
L GK V +V S IG +AKRL G S+ Y S K
Sbjct: 1 LAGK-VALVTGASRGIGRAIAKRLARDGASVVVNYASSKAA 40
>gnl|CDD|233929 TIGR02563, cas_Csy4, CRISPR-associated protein Cas6/Csy4, subtype
I-F/YPEST. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family, typified by YPO2462 of Yersinia pestis, is a
CRISPR-associated (Cas) family strictly associated with
the Ypest subtype of CRISPR/Cas locus. This family is
designated Csy4, for CRISPR/Cas Subtype Ypest protein 4
[Mobile and extrachromosomal element functions, Other].
Length = 185
Score = 27.8 bits (62), Expect = 5.7
Identities = 16/66 (24%), Positives = 22/66 (33%), Gaps = 21/66 (31%)
Query: 139 AYPLGSTLGGK------------------RVGIVGLGSIGSEVAKRLVPFGCSIAYTSRK 180
Y TLG + G+ SI SE++ VP C T R+
Sbjct: 44 LYGYQETLGRQLRLHGTAEDLDKLHSRRWLSGLSDYASI-SEIST--VPADCVKRRTVRR 100
Query: 181 KKPGVS 186
K+ S
Sbjct: 101 KQTKSS 106
>gnl|CDD|178298 PLN02695, PLN02695, GDP-D-mannose-3',5'-epimerase.
Length = 370
Score = 27.9 bits (62), Expect = 6.2
Identities = 26/92 (28%), Positives = 38/92 (41%), Gaps = 11/92 (11%)
Query: 136 DHGAYPLGSTLG--------GKRVGIVGLGS-IGSEVAKRLVPFGCSIAYTSRKKKPGVS 186
+GAY L L R+ I G G I S +A+RL G I + KK +S
Sbjct: 2 SYGAYTLA-ELEREPYWPSEKLRICITGAGGFIASHIARRLKAEGHYIIASDWKKNEHMS 60
Query: 187 YPFYANVSGLAADSDVLIVCCALTEETHHMIN 218
+ + L D V+ C +T+ H+ N
Sbjct: 61 EDMFCHEFHL-VDLRVMENCLKVTKGVDHVFN 91
>gnl|CDD|238374 cd00732, CheW, CheW, a small regulator protein, unique to the
chemotaxis signalling in prokaryotes and archea. CheW
interacts with the histidine kinase CheA, most likely
with the related regulatory domain of CheA. CheW is
proposed to form signalling arrays together with CheA
and the methyl-accepting chemotaxis proteins (MCPs),
which are involved in response modulation.
Length = 140
Score = 27.2 bits (61), Expect = 6.3
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 8/36 (22%)
Query: 91 RRGILVTNAGNAFSEDGADYVVGLLVDVLRRVSSID 126
I+V G D VVGLLVD + V +
Sbjct: 70 NTRIIVVEVG--------DQVVGLLVDSVSEVLRLS 97
>gnl|CDD|217453 pfam03251, Tymo_45kd_70kd, Tymovirus 45/70Kd protein. Tymoviruses
are single stranded RNA viruses. This family includes a
protein of unknown function that has been named based on
its molecular weight. Tymoviruses such as the ononis
yellow mosaic tymovirus encode only three proteins. Of
these two are overlapping this protein overlaps a larger
ORF that is thought to be the polymerase.
Length = 458
Score = 28.1 bits (63), Expect = 6.5
Identities = 15/60 (25%), Positives = 20/60 (33%), Gaps = 1/60 (1%)
Query: 36 DSTHSFLSRHASSVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGIL 95
+ H S + LGPSPL T P S + + RRG+L
Sbjct: 223 NQLHPLPSPQPVRHSPGI-LGPSPLHPHTTRPSPPRPAFSRSPSSPLSPLPRPSTRRGLL 281
>gnl|CDD|170080 PRK09754, PRK09754, phenylpropionate dioxygenase ferredoxin
reductase subunit; Provisional.
Length = 396
Score = 28.0 bits (62), Expect = 6.7
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 148 GKRVGIVGLGSIGSEVAKRLVPFGCSI 174
+ V IVG G+IG E+A C +
Sbjct: 144 ERSVVIVGAGTIGLELAASATQRRCKV 170
>gnl|CDD|240621 cd01620, Ala_dh_like, Alanine dehydrogenase and related
dehydrogenases. Alanine dehydrogenase/Transhydrogenase,
such as the hexameric L-alanine dehydrogenase of
Phormidium lapideum, contain 2 Rossmann fold-like
domains linked by an alpha helical region. Related
proteins include Saccharopine Dehydrogenase (SDH),
bifunctional lysine ketoglutarate reductase
/saccharopine dehydrogenase enzyme,
N(5)-(carboxyethyl)ornithine synthase, and Rubrum
transdehydrogenase. Alanine dehydrogenase (L-AlaDH)
catalyzes the NAD-dependent conversion of pyrucate to
L-alanine via reductive amination. Transhydrogenases
found in bacterial and inner mitochondrial membranes
link NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matirx side. DI contains 2
domains with Rossmann folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with one dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
classical Rossmann domains.
Length = 317
Score = 27.8 bits (62), Expect = 6.9
Identities = 25/119 (21%), Positives = 46/119 (38%), Gaps = 21/119 (17%)
Query: 137 HGAYPLGSTLGGK----------RVGIVGLGSIGSEVAKRLVPFGCSIAYTSRK------ 180
GAY L GG+ +V I+G G +G AK G ++ K
Sbjct: 141 LGAYELARIQGGRMGGAGGVPPAKVLIIGAGVVGLGAAKIAKKLGANVLVYDIKEEKLKG 200
Query: 181 -KKPGVSYPFYANVSGL---AADSDVLIVCCAL-TEETHHMINKDVMTALGKEGVIINV 234
+ G S Y+ L +D+LI + +I ++++ + + VI+++
Sbjct: 201 VETLGGSRLRYSQKEELEKELKQTDILINAILVDGPRAPILIMEELVGPMKRGAVIVDL 259
>gnl|CDD|235717 PRK06153, PRK06153, hypothetical protein; Provisional.
Length = 393
Score = 27.6 bits (62), Expect = 7.4
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 142 LGSTLGGKRVGIVGLGSIGS 161
L + L G+R+ I+GLG GS
Sbjct: 170 LSAKLEGQRIAIIGLGGTGS 189
>gnl|CDD|224626 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme [General
function prediction only].
Length = 255
Score = 27.4 bits (61), Expect = 7.6
Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 18/104 (17%)
Query: 151 VGIVGLGSIGSEVAKRL----VPFGCSIAYTSRKKK-----PGVSYPFYANVSGLAADSD 201
VGIVG G+IG + + + V F Y ++K V +++ L A+ D
Sbjct: 3 VGIVGCGAIGKFLLELVRDGRVDFELVAVYDRDEEKAKELEASVGRRCVSDIDELIAEVD 62
Query: 202 VLIVCCALTEETHHMINKDVMTAL--GKEGVIINVGRGALIDEK 243
+++ + + + V L G + ++++V GAL DE
Sbjct: 63 LVVEAA-----SPEAVREYVPKILKAGIDVIVMSV--GALADEG 99
>gnl|CDD|224997 COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy
production and conversion].
Length = 260
Score = 27.6 bits (62), Expect = 7.6
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 48 SVRAILCLGPSPLTSDTLSLLPALEIVVGSTAGIDHVDLQECRRRGILVTNAGNAFSEDG 107
S+ I+ P+ +L+ L + GS + V R+ G+ V +DG
Sbjct: 190 SLPGIMAAKKKPVKKWSLADLGLNVGLAGSPLKVVKVTPPPERKAGVKV--------KDG 241
Query: 108 ADYVVGLLVDVLRRVSSID 126
+ + LV+ L+ I
Sbjct: 242 PEEIAAELVEKLKEEGVIL 260
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 27.6 bits (62), Expect = 8.8
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 142 LGSTLGGKRVGIVGLGSIGSEVAKRL 167
LG L G RV + G G++G A++L
Sbjct: 201 LGDDLEGARVAVQGFGNVGQYAAEKL 226
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 27.6 bits (62), Expect = 8.9
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 148 GKRVGIVGLGSIGSEVAKRLVPFGCS-IAYTSRKKK 182
GK V +VG G +G + G IA T ++K
Sbjct: 167 GKWVAVVGAGGLGHMAVQYAKAMGAEVIAITRSEEK 202
>gnl|CDD|187576 cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in
this subgroup are poorly defined, one member is
identified as a putative NAD-dependent
epimerase/dehydratase. Atypical SDRs are distinct from
classical SDRs. Members of this subgroup have a
glycine-rich NAD(P)-binding motif that is related to,
but is different from, the archetypical SDRs, GXGXXG.
This subgroup also lacks most of the characteristic
active site residues of the SDRs; however, the upstream
Ser is present at the usual place, and some potential
catalytic residues are present in place of the usual
YXXXK active site motif. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 251
Score = 27.3 bits (61), Expect = 9.1
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 151 VGIVGLGSIGSEVAKRLVPFGCSIAYTSRKKKPGVSYPFYANVSGLAADSD 201
V I+G G +G +A++L+ G + T+R + + A V+ LAAD
Sbjct: 1 VLILGCGYLGQRLARQLLAQGWQVTGTTRSPEKLAADRP-AGVTPLAADLT 50
>gnl|CDD|187631 cd05373, SDR_c10, classical (c) SDR, subgroup 10. This subgroup
resembles the classical SDRs, but has an incomplete
match to the canonical glycine rich NAD-binding motif
and lacks the typical active site tetrad (instead of the
critical active site Tyr, it has Phe, but contains the
nearby Lys). SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 238
Score = 27.3 bits (61), Expect = 9.6
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 151 VGIVGLG-SIGSEVAKRLVPFGCSIAYTSRK 180
+VG G +G+ +A+R G S+A +R+
Sbjct: 2 AAVVGAGDGLGAAIARRFAAEGFSVALAARR 32
>gnl|CDD|187653 cd08950, KR_fFAS_SDR_c_like, ketoacyl reductase (KR) domain of
fungal-type fatty acid synthase (fFAS), classical
(c)-like SDRs. KR domain of fungal-type fatty acid
synthase (FAS), type I. Fungal-type FAS is a
heterododecameric FAS composed of alpha and beta
multifunctional polypeptide chains. The KR, an SDR
family member, is located centrally in the alpha chain.
KR catalyzes the NADP-dependent reduction of
ketoacyl-ACP to hydroxyacyl-ACP. KR shares the critical
active site Tyr of the Classical SDR and has partial
identity of the active site tetrad, but the upstream Asn
is replaced in KR by Met. As in other SDRs, there is a
glycine rich NAD-binding motif, but the pattern found in
KR does not match the classical SDRs, and is not
strictly conserved within this group. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 259
Score = 27.2 bits (61), Expect = 9.8
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 143 GSTLGGKRVGI--VGLGSIGSEVAKRLVPFG-CSIAYTSR 179
G + GK + G GSIG+EV L+ G I TSR
Sbjct: 2 GLSFAGKVALVTGAGPGSIGAEVVAGLLAGGATVIVTTSR 41
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 27.2 bits (61), Expect = 10.0
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 150 RVGIVGLGSIGSEVAKRL 167
+VG++GLG++GS V + L
Sbjct: 5 KVGLLGLGTVGSGVLEIL 22
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.324 0.140 0.433
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,591,489
Number of extensions: 1416974
Number of successful extensions: 1690
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1552
Number of HSP's successfully gapped: 144
Length of query: 286
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 190
Effective length of database: 6,679,618
Effective search space: 1269127420
Effective search space used: 1269127420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.0 bits)